Compositions comprising alternating 2′-modified nucleosides for use in gene modulation

ABSTRACT

The present invention provides compositions comprising at least one oligomeric compound comprising an alternating motif and further include a region that is complementary to a nucleic acid target. The compositions are useful for targeting selected nucleic acid molecules and modulating the expression of one or more genes. In preferred embodiments the compositions of the present invention hybridize to a portion of a target RNA resulting in loss of normal function of the target RNA. The present invention also provides methods for modulating gene expression.

CROSS REFERENCE TO RELATED APPLICATIONS

The present application is a continuation U.S. application Ser. No.14/834,224 filed Aug. 24, 2015, which is a continuation of U.S.application Ser. No. 10/860,265 filed Jun. 3, 2004, issued as U.S. Pat.No. 9,150,605 on Oct. 6, 2015, which is a continuation in part of U.S.application Ser. No. 10/701,007, filed Nov. 4, 2003, issued as U.S. Pat.No. 8,604,183 on Dec. 10, 2013, and also claims benefit to U.S.Provisional Applications Ser. No. 60/423,760 filed Nov. 5, 2002 and Ser.No. 60/555,521, filed Mar. 22, 2004. Each of these applications isincorporarted herein in its entirety.

SEQUENCE LISTING

The present application is being filed along with a Sequence Listing inelectronic format. The Sequence Listing is provided as a file entitledISIS5482USC2SEQ.ST25.txt, created Jun. 14, 2017, which is 196 Kb insize. The information in the electronic format of the sequence listingis incorporated herein by reference in its entirety.

FIELD OF THE INVENTION

The present invention provides modified oligomeric compounds andcompositions comprising such modified oligomeric compounds that modulategene expression. In a preferred embodiment such modulation is via theRNA interference pathway. The modified oligomeric compounds of theinvention include one or more alternating motifs that can enhancevarious physical properties and attributes compared to wild type nucleicacids. The modified oligomeric compounds are used alone or incompositions to modulate the targeted nucleic acids. The compositionsare useful for targeting selected nucleic acid molecules and modulatingthe expression of one or more genes. In preferred embodiments thecompositions of the present invention hybridize to a portion of a targetRNA resulting in loss of normal function of the target RNA.

BACKGROUND OF THE INVENTION

In many species, introduction of double-stranded RNA (dsRNA) inducespotent and specific gene silencing. This phenomenon occurs in bothplants and animals and has roles in viral defense and transposonsilencing mechanisms. This phenomenon was originally described more thana decade ago by researchers working with the petunia flower. Whiletrying to deepen the purple color of these flowers, Jorgensen et al.introduced a pigment-producing gene under the control of a powerfulpromoter. Instead of the expected deep purple color, many of the flowersappeared variegated or even white. Jorgensen named the observedphenomenon “cosuppression”, since the expression of both the introducedgene and the homologous endogenous gene was suppressed (Napoli et al.,Plant Cell, 1990, 2, 279-289; Jorgensen et al., Plant Mol. Biol., 1996,31, 957-973).

Cosuppression has since been found to occur in many species of plants,fungi, and has been particularly well characterized in Neurosporacrassa, where it is known as “quelling” (Cogoni and Macino, Genes Dev.2000, 10, 638-643; Guru, Nature, 2000, 404, 804-808).

The first evidence that dsRNA could lead to gene silencing in animalscame from work in the nematode, Caenorhabditis elegans. In 1995,researchers Guo and Kemphues were attempting to use antisense RNA toshut down expression of the par-1 gene in order to assess its function.As expected, injection of the antisense RNA disrupted expression ofpar-1, but quizzically, injection of the sense-strand control alsodisrupted expression (Guo and Kempheus, Cell, 1995, 81, 611-620). Thisresult was a puzzle until Fire et al. injected dsRNA (a mixture of bothsense and antisense strands) into C. elegans. This injection resulted inmuch more efficient silencing than injection of either the sense or theantisense strands alone. Injection of just a few molecules of dsRNA percell was sufficient to completely silence the homologous gene'sexpression. Furthermore, injection of dsRNA into the gut of the wormcaused gene silencing not only throughout the worm, but also in firstgeneration offspring (Fire et al., Nature, 1998, 391, 806-811).

The potency of this phenomenon led Timmons and Fire to explore thelimits of the dsRNA effects by feeding nematodes bacteria that had beenengineered to express dsRNA homologous to the C. elegans unc-22 gene.Surprisingly, these worms developed an unc-22 null-like phenotype(Timmons and Fire, Nature 1998, 395, 854; Timmons et al., Gene, 2001,263, 103-112). Further work showed that soaking worms in dsRNA was alsoable to induce silencing (Tabara et al., Science, 1998, 282, 430-431).PCT publication WO 01/48183 discloses methods of inhibiting expressionof a target gene in a nematode worm involving feeding to the worm a foodorganism which is capable of producing a double-stranded RNA structurehaving a nucleotide sequence substantially identical to a portion of thetarget gene following ingestion of the food organism by the nematode, orby introducing a DNA capable of producing the double-stranded RNAstructure (Bogaert et al., 2001).

The posttranscriptional gene silencing defined in Caenorhabditis elegansresulting from exposure to double-stranded RNA (dsRNA) has since beendesignated as RNA interference (RNAi). This term has come to generalizeall forms of gene silencing involving dsRNA leading to thesequence-specific reduction of endogenous targeted mRNA levels; unlikeco-suppression, in which transgenic DNA leads to silencing of both thetransgene and the endogenous gene.

Introduction of exogenous double-stranded RNA (dsRNA) intoCaenorhabditis elegans has been shown to specifically and potentlydisrupt the activity of genes containing homologous sequences.Montgomery et al. suggests that the primary interference effects ofdsRNA are post-transcriptional; this conclusion being derived fromexamination of the primary DNA sequence after dsRNA-mediatedinterference a finding of no evidence of alterations followed by studiesinvolving alteration of an upstream operon having no effect on theactivity of its downstream gene. These results argue against an effecton initiation or elongation of transcription. Finally they observed byin situ hybridization, that dsRNA-mediated interference produced asubstantial, although not complete, reduction in accumulation of nascenttranscripts in the nucleus, while cytoplasmic accumulation oftranscripts was virtually eliminated. These results indicate that theendogenous mRNA is the primary target for interference and suggest amechanism that degrades the targeted mRNA before translation can occur.It was also found that this mechanism is not dependent on the SMGsystem, an mRNA surveillance system in C. elegans responsible fortargeting and destroying aberrant messages. The authors further suggesta model of how dsRNA might function as a catalytic mechanism to targethomologous mRNAs for degradation. (Montgomery et al., Proc. Natl. Acad.Sci. USA, 1998, 95, 15502-15507).

Recently, the development of a cell-free system from syncytialblastoderm Drosophila embryos that recapitulates many of the features ofRNAi has been reported. The interference observed in this reaction issequence specific, is promoted by dsRNA but not single-stranded RNA,functions by specific mRNA degradation, and requires a minimum length ofdsRNA. Furthermore, preincubation of dsRNA potentiates its activitydemonstrating that RNAi can be mediated by sequence-specific processesin soluble reactions (Tuschl et al., Genes Dev., 1999, 13, 3191-3197).

In subsequent experiments, Tuschl et al, using the Drosophila in vitrosystem, demonstrated that 21- and 22-nt RNA fragments are thesequence-specific mediators of RNAi. These fragments, which they termedshort interfering RNAs (siRNAs) were shown to be generated by an RNaseIII-like processing reaction from long dsRNA. They also showed thatchemically synthesized siRNA duplexes with overhanging 3′ ends mediateefficient target RNA cleavage in the Drosophila lysate, and that thecleavage site is located near the center of the region spanned by theguiding siRNA. In addition, they suggest that the direction of dsRNAprocessing determines whether sense or antisense target RNA can becleaved by the siRNA-protein complex (Elbashir et al., Genes Dev., 2001,15, 188-200). Further characterization of the suppression of expressionof endogenous and heterologous genes caused by the 21-23 nucleotidesiRNAs have been investigated in several mammalian cell lines, includinghuman embryonic kidney (293) and HeLa cells (Elbashir et al., Nature,2001, 411, 494-498).

Most recently, Tijsterman et al. have shown that, in fact,single-stranded RNA oligomers of antisense polarity can be potentinducers of gene silencing. As is the case for co-suppression, theyshowed that antisense RNAs act independently of the RNAi genes rde-1 andrde-4 but require the mutator/RNAi gene mut-7 and a putative DEAD boxRNA helicase, mut-14. According to the authors, their data favor thehypothesis that gene silencing is accomplished by RNA primer extensionusing the mRNA as template, leading to dsRNA that is subsequentlydegraded suggesting that single-stranded RNA oligomers are ultimatelyresponsible for the RNAi phenomenon (Tijsterman et al., Science, 2002,295, 694-697).

Several recent publications have described the structural requirementsfor the dsRNA trigger required for RNAi activity. Recent reports haveindicated that ideal dsRNA sequences are 21nt in length containing 2 nt3′-end overhangs (Elbashir et al, EMBO (2001), 20, 6877-6887, SabineBrantl, Biochimica et Biophysica Acta, 2002, 1575, 15-25.) In thissystem, substitution of the 4 nucleosides from the 3′-end with2′-deoxynucleosides has been demonstrated to not affect activity. On theother hand, substitution with 2′-deoxynucleosides or 2′-OMe-nucleosidesthroughout the sequence (sense or antisense) was shown to be deleteriousto RNAi activity.

Investigation of the structural requirements for RNA silencing in C.elegans has demonstrated modification of the internucleotide linkage(phosphorothioate) to not interfere with activity (Parrish et al.,Molecular Cell, 2000, 6, 1077-1087.) It was also shown by Parrish etal., that chemical modification like 2′-amino or 5′-iodouridine are welltolerated in the sense strand but not the antisense strand of the dsRNAsuggesting differing roles for the 2 strands in RNAi. Base modificationsuch as guanine to inosine (where one hydrogen bond is lost) has beendemonstrated to decrease RNAi activity independently of the position ofthe modification (sense or antisense). Same “position independent” lossof activity has been observed following the introduction of mismatchesin the dsRNA trigger. Some types of modifications, for exampleintroduction of sterically demanding bases such as 5-iodoU, have beenshown to be deleterious to RNAi activity when positioned in theantisense strand, whereas modifications positioned in the sense strandwere shown to be less detrimental to RNAi activity. As was the case forthe 21 nt dsRNA sequences, RNA-DNA heteroduplexes did not serve astriggers for RNAi. However, dsRNA containing 2′-F-2′-deoxynucleosidesappeared to be efficient in triggering RNAi response independent of theposition (sense or antisense) of the 2′-F-2′-deoxynucleosides.

In one experiment the reduction of gene expression was studied usingelectroporated dsRNA and a 25mer morpholino in post implantation mouseembryos (Mellitzer et al., Mehanisms of Development, 2002, 118, 57-63).The morpholino oligomer did show activity but was not as effective asthe dsRNA.

A number of PCT applications have recently been published that relate tothe RNAi phenomenon. These include: PCT publication WO 00/44895; PCTpublication WO 00/49035; PCT publication WO 00/63364; PCT publication WO01/36641; PCT publication WO 01/36646; PCT publication WO 99/32619; PCTpublication WO 00/44914; PCT publication WO 01/29058; and PCTpublication WO 01/75164.

U.S. Pat. Nos. 5,898,031 and 6,107,094, each of which is commonly ownedwith this application and each of which is herein incorporated byreference, describe certain oligonucleotide having RNA like properties.When hybridized with RNA, these olibonucleotides serve as substrates fora dsRNase enzyme with resultant cleavage of the RNA by the enzyme.

In another recently published paper (Martinez et al., Cell, 2002, 110,563-574) it was shown that double stranded as well as single strandedsiRNA resides in the RNA-induced silencing complex (RISC) together withelF2C1 and elf2C2 (human GERp950 Argonaute proteins. The activity of5′-phosphorylated single stranded siRNA was comparable to the doublestranded siRNA in the system studied. In a related study, the inclusionof a 5′-phosphate moiety was shown to enhance activity of siRNA's invivo in Drosophila embryos (Boutla, et al., Curr. Biol., 2001, 11,1776-1780). In another study, it was reported that the 5′-phosphate wasrequired for siRNA function in human HeLa cells (Schwarz et al.,Molecular Cell, 2002, 10, 537-548).

One group of researchers looked at single strand asRNA and double strandsiRNA having 2′-0-methyl groups at select positions (Amarzguioui et al.,Nucleic Acids Research, 2003, 31(2), 589-595). They compared singlestrand asRNA wild type with 2′-O—CH₃ containing asRNA and showed thatthe 2′-O-methyl asRNA's showed good activity dependent on thepositioning of the modifications but less than wild type. When they put2′-O-methyl modified nucleosides into siRNA's they showed that thesemodifications were tolerated in smaller numbers and that there was aloss of activity with increased numbers in wings. They also showed thatsiRNA's with 2′-O-methyl modified nucleosides showed an increasedduration of activity relative to unmodified siRNA.

Another group of researchers compared asRNA and siRNA and found almostidentical target position effects, appearance of mRNA cleavage fragmentsand tolerance for mutational and chemical backbone modifications (Holenet al., et al., Nucleic Acids Research, 2003, 31(9), 2401-2407). Theyfound that small numbers of 2′-O-methyl modified nucleosides gave goodactivity compared to wild type but that the activity lessened as thenumbers of 2′-O-methyl modified nucleosides was increased.

In another recent report researchers looked at the effects of a varietyof chemical modifications, including 2′-O-methyl, had on the activityand biological properties of siRNA (Ya-Lin Chiu and Tariq M. Rana, RNA,2003, (9), 1034-1048). They showed that incorporation of 2′-O-methyl inthe sense or antisense strand (fully modified strands) severely reducedtheir activity in siRNA's relative to unmodified siRNA. Incorporationinto both strands uniformly completely abolished activity.

One group of researchers looked at the effects of 2′-O-methyl groups andother chemically modified siRNA's in mammalian cells (Braasch et al.,Biochemistry, 2003, (42), 7967-7975). They showed that fully modified2′-O—CH₃ siRNA did not inhibit gene expression in one or both strands.

In another study the placement of a 2′-O-methyl group at the 5′-terminuson the antisense strand was reported to severely limit activity whereasthe 3′-terminus of the antisense and the 3′ and 5′-termini of the sensestrand were tolerated (Czauderna et al., Nucleic Acids Research, 2003,31(11), 2705-2716). They also reported that internal 2′-O-methylsprovide nuclease stability and when placed at particular positionsinternally they show good activity but less than unmodified siRNA. Theyalso disclose siRNA constructs having alternating 2′-O-methylnucleosides in both strands.

Like the RNAse H pathway, the RNA interference pathway of antisensemodulation of gene expression is an effective means for modulating thelevels of specific gene products and may therefore prove to be uniquelyuseful in a number of therapeutic, diagnostic, and research applicationsinvolving gene silencing. The present invention therefore furtherprovides compositions useful for modulating gene expression pathways,including those relying on an antisense mechanism of action such as RNAinterference and dsRNA enzymes as well as non-antisense mechanisms. Onehaving skill in the art, once armed with this disclosure will be able,without undue experimentation, to identify preferred compositions forthese uses.

SUMMARY OF THE INVENTION

In one embodiment the present invention provides oligomeric compoundswherein each one comprises a plurality of nucleosides linked together ina sequence. The sequence comprises nucleosides of at least a first type(F) and nucleosides of a second type (S). The nucleosides can be similaror dissimilar in chemical makeup e.g., different nucleobases anddifferent in other aspects but the two types of nucleosides havedifferent 2′-substituent groups. When the 2′-substituent groups of thefirst and second types of nucleosides are other than H or OH then theoligomeric compound includes at least two nucleosides of the first typeand at least one nucleoside of the second type wherein the nucleosidesof the first type and the nucleosides of the second type are locatedwith respect to one another such that the sequence includes at least oneFSF motif. Alternatively when the 2′-substituent group of one of thefirst or the second types of nucleosides is H or OH then the oligomericcompound includes at least three nucleosides of the first type and atleast three nucleosides of the second type and the nucleosides of thefirst type and the nucleosides of the second type are located withrespect to one another such that the sequence includes at least oneFSFSFS motif.

In one embodiment the oligomeric compound has at least one portion thatis complementary to and capable of hybridizing to a selected nucleicacid target.

In another embodiment the oligomeric compound 1 further includes atleast one nucleoside of a third type (T), where the third type ofnucleoside has a different 2′-substituent group when compared to eitherof the first or second type of nucleoside.

In one embodiment the 2′-substituent groups of the first type ofnucleosides and the second type nucleosides are, independently, —F,—O—CH₂CH₂—O—CH₃, —OC₁-C₁₂ alkyl, —O—CH₂—CH₂—CH₂—NH₂, —O—(CH₂)₂—O—N(R₁)₂,—O—CH₂C(═O)—N(R₁)₂, —O—(CH₂)₂—O—(CH₂)₂, N(R₁)₂, —O—CH₂—CH₂—CH₂—NHR₁,—N₃, —O—CH₂—CH═CH₂, —NHCOR₁, —NH₂, —NHR₁, —N(R₁)₂, —SH, —SR₁, —N(H)OH,—N(H)OR₁, —N(R₁)OH, —N(R₁)OR₁ or —O—CH₂-N(H)—C(═NR₁)[N(R₁)₂];

wherein each R₁ is, independently, H, C₁-C₁₂ alkyl, a protecting groupor substituted or unsubstituted C₁-C₁₂ alkyl, C₂-C₁₂ alkenyl, or C₂-C₁₂alkynyl wherein the substituent groups are selected from halogen,hydroxyl, amino, azido, cyano, haloalkyl, alkenyl, alkoxy, thioalkoxy,haloalkoxy or aryl; and wherein the oligomeric compound includes the FSFmotif

A more preferred list of 2′-substituent groups amenable to the first andsecond type of nucleosides includes —F, —O—CH₃, —O—CH₂CH₂—O—CH₃,—O—CH₂—CH═CH₂, N₃, NH₂, NHOH, —O—(CH₂)₂—O—N(R₁)₂, —O—CH₂C(O)—N(R₁)₂,—O—CH₂—CH₂—CH₂—NH₂, —O—(CH₂)₂—O—(CH₂)₂—N(R₁)₂ or—O—CH₂—N(H)—C(═NR₁)[N(R₁)₂];

wherein each R₁ is, independently, H, C₁-C₁₂ alkyl, a protecting groupor substituted or unsubstituted C₁-C₁₂ alkyl, C₂-C₁₂ alkenyl, or C₂-C₁₂alkynyl wherein the substituent groups are selected from halogen,hydroxyl, amino, azido, cyano, haloalkyl, alkenyl, alkoxy, thioalkoxy,haloalkoxy or aryl; and wherein the oligomeric compound includes the FSFmotif.

An even more preferred list of 2′-substituent groups amenable to thefirst and second type of nucleosides includes —F, —O—CH₂CH₂—O—CH₃,—O—CH₃, —O—CH₂—CH═CH₂ or —O—CH₂—CH—CH₂—NH(R_(j)) where R_(j) is H orC₁-C₁₀ alkyl.

In an even more preferred embodiment the 2′-substituent groups of thefirst type of nucleosides and the second type nucleosides are,independently, —F, —O—CH₃ or —O—CH₂CH₂—O—CH₃.

In one embodiment, oligomeric compounds of the present invention includea nucleoside of a third type (T), the third type of nucleoside includinga 2′-substituent group that is different from the 2′-substituent groupsof either of the first or the second type of nucleosides. A preferred2′-substituent group of the third type of nucleoside is H or OH.

In one embodiment of oligomeric compounds of the present inventioninclude H or OH as one of the first or second types of nucleosides. Inthis case the minimum number of first and second type nucleosides is 3each having at least one FSFSFS motif in the resulting oligomericcompound.

In one embodiment oligomeric compounds of the present invention includea plurality of linked nucleosides linked by a phosphodiesterinternucleoside linking groups. In another embodiment theinternucleoside linking groups are phosphorothioate internucleosidelinking groups. In another embodiment the internucleoside linkinggroups, independently, phophosphodiester or phosphorothioateinternucleoside linking groups.

In one embodiment oligomeric compounds of the present invention comprisea plurality of nucleosides linked by linking groups independentlyselected from the group consisting of phosphodiester, phosphorothioate,chiral phosphorothioate, phosphorodithioate, phosphotriester,aminoalkylphosphotriester, methyl phosphonate, alkyl phosphonate,5′-alkylene phosphonate, chiral phosphonate, phosphinate,phosphoramidate, 3′-amino phosphoramidate, aminoalkylphosphoramidate,thionophosphoramidate, thionoalkylphosphonate,thionoalkylphosphotriester, selenophosphate andboranophosphate.phosphodiester and phosphorothioate.

In one embodiment the oligomeric compounds of the present inventioncomprise at least one motif selected from F(SF)_(n)(S)_(nn) where n isfrom 2 to about 20 and nn is 0 or 1. In a further embodiment oligomericcompounds of the present invention comprise at least two motifsindependently selected from F(SF)_(n)(S)_(nn) where n is from 1 to about20 and nn is 0 or 1. In a preferred embodiment oligomeric compoundscomprise 2 motifs selected from F(SF)_(n)(S)_(nn) where n is from 1 toabout 20 and nn is 0 or 1, and the two motifs are further separated by aregion comprising a sequence of nucleosides. In an even more preferredembodiment the sequence of nucleosides is joined together such that oneof the motifs is located at the 5′-end of the sequence of nucleosidesand the other of the motifs is located at the 3′-end of the sequence ofnucleosides and the motifs being separated by from about 6 to about 20nucleosides.

In one embodiment the oligomeric compounds of the present invention havethe formula X₁—Y—X₂:

-   -   wherein        -   Y is a region of from about 6 to about 18 linked            nucleosides; and        -   each of X₁ and X₂ is, independently, a plurality of linked            nucleosides having the formula F(SF)_(n)(S)_(nn) where n is            from 1 to about 20 and nn is 0 or 1.    -   In a preferred embodiment each of X₁ and X₂ is, independently,        FSFS, FSFSF, FSFSFS, FSFSFSF or FSFSFSFS. In a further preferred        embodiment Y is from about 5 to about 12 linked nucleosides. In        another embodiment each of the linked nucleosides is linked by a        phosphodiester internucleoside linkage. In another embodiment        each of the linked nucleosides is linked by a phosphorothioate        internucleoside linkage. And in an even further embodiment each        of the linked nucleosides is, independently, linked by a        phophosphodiester or a phosphorothioate internucleoside linkage.        In another embodiment the linked nucleosides selected from        F(SF)_(n)(S)_(nm) are linked by phosphodiester internucleoside        linkages, the linked nucleosides comprising the Y region are        linked by phosphorothioate internucleoside linkages and each of        the F(SF)_(n)(S)_(nn) motifs are independently linked to the        ends of the Y region by a phosphodiester or phosphorothioate        internucleoside linkage. In an even further embodiment the        linked nucleosides selected from F(SF)_(n)(S)_(nn) are linked by        phosphorothioate internucleoside linkages, the linked        nucleosides comprising the Y region are linked by phosphodiester        internucleoside linkages and each of the F(SF)_(n)(S)_(nn)        motifs are independently linked to the ends of the Y region by a        phosphodiester or phosphorothioate internucleoside linkage.

In one embodiment the oligomeric compounds of the present inventioncomprise from about 10 to about 40 nucleotides. In a more preferredembodiment the oligomeric compounds of the present invention comprisefrom about 18 to about 30 nucleotides. In an even more preferredembodiment the oligomeric compounds of the present invention comprisefrom 21 to about 24 nucleotides.

In one embodiment the oligomeric compounds of the present inventioncomprise at least one conjugate group. In a preferred embodiment theconjugate group is a terminal cap moiety. In another preferredembodiment the conjugate group is attached to one or both of the3′-terminal and 5′-terminal ends of the oligomeric compound. In an evenmore preferred embodiment the terminal cap moiety is an inverted deoxyabasic moiety.

In one embodiment of the present invention compositions are providedcomprising a first oligomeric compound and a second oligomeric compoundwhere at least a portion of the first oligomeric compound is capable ofhybridizing with at least a portion of the second oligomeric compoundand at least a portion of the first oligomeric compound is complementaryto and capable of hybridizing to a selected nucleic acid target. Atleast one of the first and the second oligomeric compounds comprise atleast nucleosides of a first type (F) and nucleosides of a second type(S). The first and the second types of nucleosides differing in at leastone aspect from one another in that they have different 2′-substituentgroups. When the 2′-substituent groups of the first and the second typesof nucleosides are other than H or OH then at least one of the first andthe second oligomeric compounds includes at least two nucleosides of thefirst type and at least one nucleoside of the second type wherein thenucleosides of the first type and the nucleosides of the second type arelocated with respect to one another such that the first or secondoligomeric compound includes at least one FSF motif. When the2′-substituent group of one of the first or the second type ofnucleoside is H or OH then at least one of the first and the secondoligomeric compounds includes at least three nucleosides of the firsttype and at least three nucleosides of the second type and thenucleosides of the first type and the nucleosides of the second type arelocated with respect to one another such that at least one of the firstand the second oligomeric compounds includes at least one FSFSFS motif.

In one embodiment of the present invention compositions comprise atleast one of said first and second oligomeric compounds having at leasttwo nucleosides of a first type and at least two nucleosides of a secondtype and wherein the 2′-substituent groups are other 2′-H and 2′-OHthereby providing a composition having at least one of said first andsaid second oligomeric compound having at least one FSFS motif. In afurther embodiment there are at least three nucleosides of said firsttype and at least two nucleosides of said second type to give a t leastone of said first and said second oligomeric compound having at leastone FSFSF motif

In one embodiment the compositions of the present invention at least oneof the first and the second oligomeric compounds comprise onlynucleosides of the first type and nucleosides of the second type andwherein the nucleosides of the first and the second types arealternating throughout the entire sequence of the oligomeric compound.In a further embodiment both of the first and the second oligomericcompounds comprise only nucleosides of the first type and nucleosides ofthe second type and wherein the nucleosides of the first and the secondtypes are alternating throughout the entire sequence of both of theoligomeric compounds.

In one embodiment the compositions of the present invention comprise athird type of nucleoside (T) that is different than said first and saidsecond type of nucleosides. In a preferred embodiment the 2′-substituentgroup of the third type nucleoside is 2′-H or 2′-OH.

In one embodiment the 2′-substituent groups of the first and the secondtypes of nucleosides are, independently, —F, —O—CH ₂CH₂—O—CH₃, —OC₁-C₁₂alkyl, —O—CH₂—CH₂—CH₂—NH₂, —O—(CH₂)₂—O—N(R₁)₂, —O—CH₂C(═O)—N(R₁)₂,—O—(CH₂)₂—O—(CH₂)₂—N(R₁)₂, —O—CH₂—CH₂—CH₂—NHR₁, —N₃, —O—CH₂—CH═CH₂,—NHCOR₁, —NH₂, —NHR₁, —N(R₁)₂, —SH, —SR₁, —N(H)OH, —N(H)OR₁, —N(R₁)OH,—N(R₁)OR₁ or —O—CH₂—N(H)—C(═NR₁)[N(R₁)₂]; wherein each R₁ is,independently, H, C₁-C₁₂ alkyl, a protecting group or substituted orunsubstituted C₁-C₁₂ alkyl, C₂-C₁₂ alkenyl, or C₂-C₁₂ alkynyl whereinthe substituent groups are selected from halogen, hydroxyl, amino,azido, cyano, haloalkyl, alkenyl, alkoxy, thioalkoxy, haloalkoxy oraryl. A more preferred list of 2′-substituent groups of the first andthe second types of nucleosides are, independently, —F, —O—CH₃,—O—CH₂CH₂—O—CH₃, —O—CH₂—CH═CH₂, N₃, NH₂, NHOH, —O—(CH₂)₂—O—N(R₁)₂,—O—CH₂C(O)—N(R₁)₂, —O—CH₂—CH₂—CH₂—NH₂, —O—(CH₂)₂—O—(CH₂)₂—N(R₁)₂ or—O—CH₂—N(H)—C(═NR₁)[N(R₁)₂];

-   -   wherein each R₁ is, independently, H, C₁-C₁₂ alkyl, a protecting        group or substituted or unsubstituted C₁-C₁₂ alkyl, C₂-C₁₂        alkenyl, or C₂-C₁₂ alkynyl wherein the substituent groups are        selected from halogen, hydroxyl, amino, azido, cyano, haloalkyl,        alkenyl, alkoxy, thioalkoxy, haloalkoxy or aryl wherein the        oligomeric compound includes the FSF motif.

An even more preferred list of 2′-substituent groups of the first andthe second types of nucleosides includes —F, —O—CH₂CH₂—O—-CH₃, —O—CH₃,—O—CH₂—CH═CH₂ or —O—CH₂—CH—CH₂—NH(R_(j)) where R_(j) is H or C₁-C₁₀alkyl.

A preferred list of 2′-substituent groups of the first and the secondtypes of nucleosides includes —F, —O—CH₃ or —O—CH₂CH₂—O—CH₃. With —F or—O—CH₃ being an even more preferred list.

In one embodiment each of the first and the second type of nucleosideshave 3′-endo conformational geometry.

In one embodiment, the compositions of the present invention includefirst type of nucleosides that are 2′-OH nucleosides. In anotherembodiment the first type nucleoside is 2′-H nucleoside. In anotherembodiment the second type nucleoside is a 2′-F nucleoside. In evenanother embodiment the second type nucleoside is a 2′-O—CH₃ nucleoside.In another embodiment the first type of nucleosides are 2′-fluoronucleosides and the second type of nucleosides are 2′-O—CH₃ nucleosides.

In one embodiment of the present invention the first oligomeric compoundfurther comprises a 5′-phosphate group. In another embodiment the secondoligomeric compound further comprises a 5′-phosphate group. In even afurther embodiment each of the first and the second oligomeric compoundsindependently, comprise a 5′-phosphate group. In an even furtherembodiment the first oligomeric compound comprises a 3′-terminal OHgroup.

In one embodiment of the present invention compositions the nucleosidesof each of the first and the second oligomeric compounds are linked byphosphodiester internucleoside linking groups. In another embodiment thenucleosides of each of the first and the second oligomeric compounds arelinked by phosphorothioate internucleoside linking groups. In an evenfurther embodiment the nucleosides of one the first and the secondoligomeric compound are linked by phosphorothioate internucleosidelinking groups and the nucleosides of the other of the first and thesecond oligomeric compound are linked by phosphodiester internucleosidelinking groups. In a further embodiment the nucleosides of the firstoligomeric compound are linked by phosphorothioate internucleosidelinking groups and the nucleosides of the second oligomeric compound arelinked by phosphodiester internucleoside linking groups. In an evenfurther embodiment each of the nucleosides of the first and the secondoligomeric compound are independently linked by phosphorothioate orphosphodiester internucleoside linking groups.

In one embodiment of the present invention each of the nucleosides ofthe first and the second oligomeric compound are independently linked byan internucleoside linking group selected from the group consisting ofphosphodiester, phosphorothioate, chiral phosphorothioate,phosphorodithioate, phosphotriester, aminoalkylphosphotriester, methylphosphonate, alkyl phosphonate, 5′-alkylene phosphonate, chiralphosphonate, phosphinate, phosphoramidate, 3′-amino phosphoramidate,aminoalkylphosphoramidate, thionophosphoramidate,thionoalkylphosphonate, thionoalkylphosphotriester, selenophosphate andboranophosphate.

In one embodiment each of the first and the second oligomeric compoundscomprise only the first and the second type nucleosides and wherein thefirst and the second type nucleosides are alternating in both of thefirst and the second oligomeric compounds wherein preferred first typenucleosides comprise 2′-F or 2′-O—CH₃ groups. In a preferred embodimentthe first type nucleosides comprises one of 2′-F or 2′-O—CH₃ groups andthe second type nucleosides comprise the other of 2′-F or 2′-O—CH₃groups with 2′-F or 2′-O—CH₃ groups preferred for the first typenucleosides. In a preferred embodiment the first oligomeric compound hasfirst type nucleosides starting at its 5′-terminus and wherein the firsttype nucleosides of the first and the second oligomeric compounds alignwith each other when the first and second oligomeric compounds arehybridized. In another preferred embodiment the first oligomericcompound has first type nucleosides starting at its 5′-terminus whereinthe first type nucleosides of the first oligomeric compound and thesecond type nucleosides of the second oligomeric compound align witheach other when the first and the second oligomeric compounds arehybridized.

In one embodiment of the present invention when the first and secondoligomeric compounds comprise only the first and second type nucleosidesand where the first and second type nucleosides are alternating in bothof the first and the second oligomeric compounds the first typenucleosides comprises one of 2′-F or 2′-O—CH₃ groups and the second typenucleosides comprise the other of 2′-F or 2′-O—CH₃ groups. In apreferred embodiment the nucleosides of the first oligomeric compoundare linked with phosphorothioate internucleoside linking groups. Inanother preferred embodiment the nucleosides of the second oligomericcompound are linked with phosphodiester internucleoside linking groups.

In one embodiment compositions of the present invention comprise atleast one conjugate group. In a preferred embodiment the conjugate groupis attached at the 3′-end, the 5′-end or both the 3′-end and the 5′-endof one of the first and second oligomeric compounds. In a more preferredembodiment the conjugate group comprises a terminal cap moiety. In aneven more preferred embodiment the terminal cap moiety is an inverteddeoxy abasic moiety. In a more preferred embodiment one of the first andsecond oligomeric compounds is a sense strand and wherein the sensestrand comprises a terminal cap moiety at one or both of the 3′-terminaland the 5′-terminal ends wherein a preferred terminal cap moiety is aninverted deoxy abasic moiety.

In one embodiment of the present invention the first and the secondoligomeric compounds are a complementary pair of siRNA oligonucleotides.

In one embodiment at least one of the first or second oligomericcompounds comprise at least one motif selected from F(SF)_(n)(S)_(nn),where n is from 2 to about 20 and nn is 0 or 1. In a preferredembodiment at least one of the first or second oligomeric compoundscomprises at least two motifs independently selected fromF(SF)_(n)(S)_(nn) where n is from 2 to about 20 and nn is 0 or 1. In aneven more preferred embodiment the two motifs are separated by a regioncomprising a sequence of nucleosides. In another preferred embodimentone of the two motifs are located at the 5′-end of one of the first orsecond oligomeric compounds and the second of the two motifs is locatedat the 3′-end of the same oligomeric compound and wherein from about 6to about 20 nucleosides are located between the motifs. In a preferredembodiment the first or second oligomeric compound having the motifs hasthe formula: X₃−Y₂−X₄:

-   -   wherein Y₂ is a region of from about 6 to about 18 linked        nucleosides and each of X₃ and X₄ is, independently, a plurality        of linked nucleosides having the formula (SF)_(n)(S)_(nn) where        n is from 2 to about 20 and nn is 0 or 1; and nn is from 1 to        about 3.    -    In a preferred embodiment each of X₃ and X₄ is, independently,        FSFS, FSFSF, FSFSFS, FSFSFSF or FSFSFSF S. In another preferred        embodiment Y₂ is from about 5 to about 12 linked nucleosides.    -    In a preferred embodiment each of the linked nucleosides is        linked by a phosphodiester internucleoside linkage. In a further        preferred each of the linked nucleosides is linked by a        phosphorothioate internucleoside linkage and in another        preferred embodiment each of the linked nucleosides is,        independently, linked by a phosphodiester or a phosphorothioate        internucleoside linkage.

In a further embodiment the linked nucleosides selected fromF(SF)_(n)(S)_(nn) are linked by phosphodiester internucleoside linkages,the linked nucleosides comprising the Y region are linked byphosphorothioate internucleoside linkages and each of theF(SF)_(n)(S)_(nn) motifs are independently linked to the ends of the Yregion by a phosphodiester or phosphorothioate internucleoside linkage.In a further embodiment the linked nucleosides selected fromF(SF)_(n)(S)_(nn) are linked by phosphorothioate internucleosidelinkages, the linked nucleosides comprising the Y region are linked byphosphodiester internucleoside linkages and each of theF(SF)_(n)(S)_(nn) motifs are independently linked to the ends of the Yregion by a phosphodiester or phosphorothioate internucleoside linkage.

In one embodiment compositions of the present invention comprise firstand the second oligomeric compounds that are an antisense/sense pair ofoligonucleotides.

In one embodiment compositions are provided wherein each of the firstand second oligomeric compounds has from about about 8 to about 80nucleotides. In other embodiments, the oligomeric compounds have fromabout 12 to about 30 nucleotides. In yet other embodiments, theoligomeric compounds have from about 12 to about 24 nucleotides. Incertain preferred embodiments, the oligomeric compounds have from about19 to about 23 nucleotides.

In one embodiment compositions are provided wherein the first oligomericcompound is an antisense oligonucleotide.

In one embodiment compositions are provided wherein the secondoligomeric compound is a sense oligonucleotide.

In one embodiment methods are provided inhibiting gene expressioncomprising contacting one or more cells, a tissue or an animal with acomposition of the invention.

In one embodiment methods are provided inhibiting gene expressioncomprising contacting one or more cells, a tissue or an animal with anoligomeric compound of the invention.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides single and double stranded compositionscomprising at least one alternating motif Alternating motifs of thepresent invention have the formula F(SF)_(n)(S)_(nn) where F is anucleoside of a first type, S is a nucleoside of a second type, n isfrom 1 to about 20 and nn is 0 or 1. Each of the types of nucleosideshave identical 2′-substituent groups with the two types beingdifferentiated from each other in that at least the 2′-substituentgroups are different. H and OH are not used in the alternating motifuntil there are at least 3 of each type of nucleosides present therebyforming a FSFSFS or larger run of alternating nucleosides in which caseone of the first and second types of nucleosides can be H or OH. Thealternating motifs can be present in one more regions of a singlestranded oligomeric compound or can be found in one or more regions intwo oligomeric compounds forming a double stranded composition of theinvention.

In one aspect of the present invention the compositions comprise aregion of complementarity to a nucleic acid target. The complementaryregion can comprise a continuous sequence of nucleosides bound byinternucleoside linkages or can comprise multiple regions that areinterrupted by secondary structures such as a loops thereby forming acomplementary region from two or more non-continuous regions of the sameoligomeric compound. Double stranded regions of the compositions of thepresent invention can be formed from two oligomeric compounds hybridizedtogether or from a single oligomeric compound that has a region of selfcomplementarity.

In another aspect of the present invention oligomeric compounds areprovided comprising at least one alternating motif. These oligomericcompounds are useful as asRNAs in the RNAi pathway. In the context ofthe present invention an “asRNA” is an antisense RNA oligomeric compoundthat is not duplexed with another separate oligonucleotide such as asense strand but may contain duplexed regions formed between adjacentcomplementary regions. In one aspect the compositions comprisingalternating motifs of the present invention mimic RNA by incorporatingregions of nucleosides having 3′-endo conformational geometry andenhance desired properties such as but not limited to modulation ofpharmacokinetic properties through modification of protein binding,protein off-rate, absorption and clearance; modulation of nucleasestability as well as chemical stability; modulation of the bindingaffinity and specificity of the oligomer (affinity and specificity forenzymes as well as for complementary sequences); and increasing efficacyof RNA cleavage.

In one aspect of the present invention compositions are providedcomprising a first and a second oligomeric compound that are at leastpartially hybridized to form a duplex region and further comprising aregion that is complementary to and hybridizes to a nucleic acid target.Each of the compositions of the invention comprise at least onealternating motif. In one aspect the compositions include a firstoligomeric compound that is an antisense strand having a complementaryregion to a nucleic acid target and a second oligomeric compound that isa sense strand having one or more regions of complementarity to andforming at least one duplex region with the first oligomeric compound.At least one alternating motif is located on either the first or secondoligomeric compound.

Compositions of the present invention also include single and doublestranded constructs that comprise at least two regions of alternatingnucleosides in one or both of the strands. These alternating regions cancomprise up to about 40 nucleosides but preferable comprise from about 3to about 9 nucleosides. In a preferred embodiment the regions ofalternating nucleosides are located at the termini of one or botholigomeric compounds in an oligomeric compound or composition of theinvention. In an even more preferred embodiment an oligomeric compoundof the invention comprises from 4 to about 8 nucleosides of alternatingnucleosides at each termini (3′ and 5′) and these regions are separatedby from about 5 to about 12 linked nucleosides.

Some representative duplexed constructs amenable to the presentinvention are shown below:

(SEQ ID NO.: 53) 5′-NN NNN NN N N(N)n NNN  NNN NNN-3′ as(SEQ ID NO.: 53) 3′-NN NNN NN N N(N)n NN N NNN NNN-5′ s (SEQ ID NO.: 53)5′-NN NNN NN N N(N)n NN N NNN NNN-3′ as (SEQ ID NO.: 53)3′-NN NNN NNN N(N)n N NN NNN NNN-5′ s (SEQ ID NO.: 53) 5′-NN NNN NNN N(N)n NNN NNN NNN-3′ as (SEQ ID NO.: 53) 3′-NN NNN NNN N(N)n NNN NNN NNN-5′ s (SEQ ID NO.: 53) 5′-N NNN NNN N(N)n NNN NNN NNN-3′ as (SEQ ID NO.: 53) 3′-N NNN NNN N(N)n NNN NNN NNN-5′ s (SEQ ID NO.: 53) 5′-N NNN NNN N(N)n NNN NNN NNN-3′ as (SEQ ID NO.: 53) 3′-N NNN NNN N(N)n NNN NNN NNN-5′ s (SEQ ID NO.: 53) 5′-N NNN NNN N(N)n NNN NNN NNN-3′ as (SEQ ID NO.: 53) 3′-N NNN NN N N(N)n NNN NNN NNN-5′ s

The underlined regions represent linked nucleosides that can be uniformor modified. Essentially the underlined region can be described as beingthe gap and is shown being variable with n being generally from about 1to about 40 but from 1 to about 4 being preferred. The alternatingregions are shown in bold. These examples are meant to be representativeand not limiting. The alternating nucleosides can be aligned on the twostrands such as for example all the modifications in the alternatingregions of the sense strand strand are paired with identicalmodifications in the antisense strand or alternatively the registers canbe offset with the like modifications in the alternating regions of onestrand pairing with unlike modifications in the other strand. Anotheroption is to have dissimilar modifications in each of the strands whichwould not lead to an aligned or misaligned register.

Preferred 2′-modifications for the alternating regions comprise allpossible orientations of OMe, MOE, OH, F, deoxy, ara OH, ara F withbackbone either full PO or Full PS throughout or PO/PS either in wingsor gap and the other of PO/PS in the other of the wings or the gap.

Compositions of the present invention are useful for the modulation ofgene expression. In one aspect of the present invention a targeted cell,group of cells, a tissue or an animal is contacted with a composition ofthe invention to effect reduction of mRNA that can directly inhibit geneexpression. In another embodiment the reduction of mRNA indirectlyupregulates a non-targeted gene through a pathway that relates thetargeted gene to a non-targeted gene. Numerous methods and models forthe regulation of genes using compositions of the invention areillustrated in the examples.

Compositions of the invention modulate gene expression by hybridizing toa nucleic acid target resulting in loss of its normal function. As usedherein, the term “target nucleic acid” or “nucleic acid target” is usedfor convenience to encompass any nucleic acid capable of being targetedincluding without limitation DNA, RNA (including pre-mRNA and mRNA orportions thereof) transcribed from such DNA, and also cDNA derived fromsuch RNA. In a preferred embodiment of the invention the target nucleicacid is a messenger RNA. In a further preferred embodiment thedegradation of the targeted messenger RNA is facilitated by a RISCcomplex that is formed with compositions of the invention. In anotherpreferred embodiment the degradation of the targeted messenger RNA isfacilitated by a nuclease such as RNaseH.

The hybridization of a composition of the invention with its targetnucleic acid is generally referred to as “antisense”. Consequently, thepreferred mechanism in the practice of some preferred embodiments of theinvention is referred to herein as “antisense inhibition.” Suchantisense inhibition is typically based upon hydrogen bonding-basedhybridization of oligonucleotide strands or segments such that at leastone strand or segment is cleaved, degraded, or otherwise renderedinoperable. In this regard, it is presently preferred to target specificnucleic acid molecules and their functions for such antisenseinhibition.

The functions of DNA to be interfered with can include replication andtranscription. Replication and transcription, for example, can be froman endogenous cellular template, a vector, a plasmid construct orotherwise. The functions of RNA to be interfered with can includefunctions such as translocation of the RNA to a site of proteintranslation, translocation of the RNA to sites within the cell which aredistant from the site of RNA synthesis, translation of protein from theRNA, splicing of the RNA to yield one or more RNA species, and catalyticactivity or complex formation involving the RNA which may be engaged inor facilitated by the RNA. In the context of the present invention,“modulation” and “modulation of expression” mean either an increase(stimulation) or a decrease (inhibition) in the amount or levels of anucleic acid molecule encoding the gene, e.g., DNA or RNA. Inhibition isoften the preferred form of modulation of expression and mRNA is often apreferred target nucleic acid.

The compositions and methods of the present invention are also useful inthe study, characterization, validation and modulation of smallnon-coding RNAs. These include, but are not limited to, microRNAs(miRNA), small nuclear RNAs (snRNA), small nucleolar RNAs (snoRNA),small temporal RNAs (stRNA) and tiny non-coding RNAs (tncRNA) or theirprecursors or processed transcripts or their association with othercellular components.

Small non-coding RNAs have been shown to function in variousdevelopmental and regulatory pathways in a wide range of organisms,including plants, nematodes and mammals. MicroRNAs are small non-codingRNAs that are processed from larger precursors by enzymatic cleavage andinhibit translation of mRNAs. stRNAs, while processed from precursorsmuch like miRNAs, have been shown to be involved in developmental timingregulation. Other non-coding small RNAs are involved in events asdiverse as cellular splicing of transcripts, translation, transport, andchromosome organization.

As modulators of small non-coding RNA function, the compositions of thepresent invention find utility in the control and manipulation ofcellular functions or processes such as regulation of splicing,chromosome packaging or methylation, control of developmental timingevents, increase or decrease of target RNA expression levels dependingon the timing of delivery into the specific biological pathway andtranslational or transcriptional control. In addition, the compositionsof the present invention can be modified in order to optimize theireffects in certain cellular compartments, such as the cytoplasm,nucleus, nucleolus or mitochondria.

The compositions of the present invention can further be used toidentify components of regulatory pathways of RNA processing ormetabolism as well as in screening assays or devices.

Oligomeric Compounds

In the context of this invention, the term “oligomeric compound” refersto a plurality of naturally-occurring and or non-naturally-occurringmonomeric units joined together in a specific sequence. This termincludes oligonucleotides, oligonucleosides, oligonucleotide analogs,oligonucleotide mimetics and combinations of these. Oligomeric compoundsare typically structurally distinguishable from, yet functionallyinterchangeable with, naturally-occurring or synthetic wild-typeoligonucleotides. Thus, oligomeric compounds include all such structuresthat function effectively to mimic the structure and/or function of adesired RNA or DNA strand, for example, by hybridizing to a target.

Oligomeric compounds are routinely prepared linearly but can be joinedor otherwise prepared to be circular and may also include branching.Oligomeric compounds can included double stranded constructs such as forexample two strands hybridized to form double stranded compounds. Thedouble stranded compounds can be linked or separate and can includeoverhangs on the ends. In general an oligomeric compound comprises abackbone of linked momeric subunits where each linked momeric subunit isdirectly or indirectly attached to a heterocyclic base moiety.Oligomeric compounds may also include monomeric subunits that are notlinked to a heterocyclic base moiety thereby providing abasic sites. Thelinkages joining the monomeric subunits, the sugar moieties orsurrogates and the heterocyclic base moieties can be independentlymodified giving rise to a plurality of motifs for the resultingoligomeric compounds including hemimers, gapmers and chimeras.

In the context of this invention, the term “oligonucleotide” refers toan oligomer or polymer of ribonucleic acid (RNA) or deoxyribonucleicacid (DNA) or mimetics thereof. This term includes oligonucleotidescomposed of naturally-occurring nucleobases, sugars and covalentinternucleoside (backbone) linkages as well as oligonucleotides havingnon-naturally-occurring portions that function similarly. Such modifiedor substituted oligonucleotides are often preferred over native formsbecause of desirable properties such as, for example, enhanced cellularuptake, enhanced affinity for nucleic acid target and increasedstability in the presence of nucleases.

Included in preferred oligomeric compounds are oligonucleotides such asantisense oligonucleotides, antisense oligonucleotides, ribozymes,external guide sequence (EGS) oligonucleotides, alternate splicers,primers, probes, and other oligonucleotides which hybridize to at leasta portion of the target nucleic acid. As such, these oligonucleotidesmay be introduced in the form of single-stranded, double-stranded,circular or hairpin oligonucleotides and may contain structural elementssuch as internal or terminal bulges or loops. Once introduced to asystem, the compositions of the invention may elicit the action of oneor more enzymes or structural proteins to effect modification of thetarget nucleic acid.

One non-limiting example of such an enzyme is RNAse H, a cellularendonuclease which cleaves the RNA strand of an RNA:DNA duplex. It isknown in the art that single-stranded antisense oligonucleotides whichare “DNA-like” elicit RNAse H. Activation of RNase H, therefore, resultsin cleavage of the RNA target, thereby greatly enhancing the efficiencyof oligonucleotide-mediated inhibition of gene expression. Similar roleshave been postulated for other ribonucleases such as those in the RNaseIII and ribonuclease L family of enzymes.

While the preferred form of antisense oligonucleotide is asingle-stranded antisense oligonucleotide, in many species theintroduction of double-stranded structures, such as double-stranded RNA(dsRNA) molecules, has been shown to induce potent and specificantisense-mediated reduction of the function of a gene or its associatedgene products. This phenomenon occurs in both plants and animals and isbelieved to have an evolutionary connection to viral defense andtransposon silencing.

In the context of this invention, the term “ oligonucleotide” refers toa sequence of nucleosides that are joined by internucleoside linkagesthat do not have phosphorus atoms. Internucleoside linkages of this typeinclude short chain alkyl, cycloalkyl, mixed heteroatom alkyl, mixedheteroatom cycloalkyl, one or more short chain heteroatomic and one ormore short chain heterocyclic. These internucleoside linkages includebut are not limited to siloxane, sulfide, sulfoxide, sulfone, acetyl,formacetyl, thioformacetyl, methylene formacetyl, thioformacetyl,alkeneyl, sulfamate; methyleneimino, methylenehydrazino, sulfonate,sulfonamide, amide and others having mixed N, O, S and CH₂ componentparts.

Representative United States patents that teach the preparation of theabove oligonucleosides include, but are not limited to, U.S. Pat. Nos.5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141; 5,235,033;5,264,562; 5,264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967;5,489,677; 5,541,307; 5,561,225; 5,596,086; 5,602,240; 5,610,289;5,602,240; 5,608,046; 5,610,289; 5,618,704; 5,623,070; 5,663,312;5,633,360; 5,677,437; 5,792,608; 5,646,269 and 5,677,439, certain ofwhich are commonly owned with this application, and each of which isherein incorporated by reference.

In addition to the modifications described above, the nucleosides of thecompositions of the invention can have a variety of other modificationso long as these other modifications either alone or in combination withother nucleosides enhance one or more of the desired propertiesdescribed above. Thus, for nucleotides that are incorporated intocompositions of the invention, these nucleotides can have sugar portionsthat correspond to naturally-occurring sugars or modified sugars.Representative modified sugars include carbocyclic or acyclic sugars,sugars having substituent groups at one or more of their 2′, 3′ or 4′positions and sugars having substituents in place of one or morehydrogen atoms of the sugar. Additional nucleosides amenable to thepresent invention having altered base moieties and or altered sugarmoieties are disclosed in U.S. Pat. No. 3,687,808 and PCT applicationPCT/US89/02323.

Oligomeric compounds having altered base moieties or altered sugarmoieties are also included in the present invention. All such modifiedoligomeric compounds are comprehended by this invention so long as theyfunction effectively to mimic the structure of a desired RNA or DNAstrand. A class of representative base modifications include tricycliccytosine analog, termed “G clamp” (Lin, et al., J. Am. Chem. Soc. 1998,120, 8531). This analog makes four hydrogen bonds to a complementaryguanine (G) within a helix by simultaneously recognizing theWatson-Crick and Hoogsteen faces of the targeted G. This G clampmodification when incorporated into phosphorothioate oligonucleotides,dramatically enhances antisense potencies in cell culture. Thecompositions of the invention also can include phenoxazine-substitutedbases of the type disclosed by Flanagan, et al., Nat. Biotechnol. 1999,17(1), 48-52.

The oligomeric compounds in accordance with this invention preferablycomprise from about 8 to about 80 nucleobases (i.e. from about 8 toabout 80 linked nucleosides and/or monomeric subunits). One of ordinaryskill in the art will appreciate that the invention embodies oligomericcompounds of 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58,59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76,77, 78, 79, or 80 nucleobases in length.

In one preferred embodiment, the oligomeric compounds of the inventionare 10 to 50 nucleobases in length. One having ordinary skill in the artwill appreciate that this embodies oligomeric compounds of 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30,31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48,49, or 50 nucleobases in length.

In another preferred embodiment, the oligomeric compounds of theinvention are 12 to 30 nucleobases in length. One having ordinary skillin the art will appreciate that this embodies oligomeric compounds of12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,or 30 nucleobases in length.

In a further preferred embodiment, the oligomeric compounds of theinvention are 12 to 24 nucleobases in length. One having ordinary skillin the art will appreciate that this embodies oligomeric compounds of12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 or 24 nucleobases inlength.

In another preferred embodiment, the oligomeric compounds of theinvention are 19 to 23 nucleobases in length. One having ordinary skillin the art will appreciate that this embodies oligomeric compounds of19, 20, 21, 22 or 23 nucleobases in length.

One particularly preferred length for oligomeric compounds is from about12 to about 30 nucleobases. Another particularly preferred length isfrom about 12 to about 24 nucleobases. A further particularly preferredlength is from about 19 to about 23 nucleobases.

Chimeric Oligomeric Compounds

It is not necessary for all positions in an oligomeric compound to beuniformly modified, and in fact more than one of the aforementionedmodifications may be incorporated in a single oligomeric compound oreven at a single monomeric subunit such as a nucleoside within aoligonucleotide. The present invention also includes chimeric oligomericcompounds such as chimeric oligonucleotides. “Chimeric” oligomericcompounds or “chimeras,” in the context of this invention, areoligomeric compounds such as oligonucleotides containing two or morechemically distinct regions, each made up of at least one monomer unit,i.e., a nucleotide in the case of a nucleic acid based oligomer.

Chimeric oligonucleotides typically contain at least one region modifiedso as to confer increased resistance to nuclease degradation, increasedcellular uptake, and/or increased binding affinity for the targetnucleic acid. An additional region of the oligonucleotide may serve as asubstrate for enzymes capable of cleaving RNA:DNA or RNA:RNA hybrids. Byway of example, RNase H is a cellular endonuclease which cleaves the RNAstrand of an RNA:DNA duplex. Activation of RNase H, therefore, resultsin cleavage of the RNA target, thereby greatly enhancing the efficiencyof inhibition of gene expression. Consequently, comparable results canoften be obtained with shorter oligonucleotides when chimeras are used,compared to for example phosphorothioate deoxyoligonucleotideshybridizing to the same target region. Cleavage of the RNA target can beroutinely detected by gel electrophoresis and, if necessary, associatednucleic acid hybridization techniques known in the art.

Chimeric compositions of the invention may be formed as compositestructures of two or more oligomeric compounds such as oligonucleotides,oligonucleotide analogs, oligonucleosides and/or oligonucleotidemimetics as described above. Such oligomeric compounds have also beenreferred to in the art as hybrids hemimers, gapmers or inverted gapmers.Representative United States patents that teach the preparation of suchhybrid structures include, but are not limited to, U.S. Pat. Nos.5,013,830; 5,149,797; 5,220,007; 5,256,775; 5,366,878; 5,403,711;5,491,133; 5,565,350; 5,623,065; 5,652,355; 5,652,356; and 5,700,922,certain of which are commonly owned with the instant application, andeach of which is herein incorporated by reference in its entirety.

Oligomer Mimetics

Another preferred group of oligomeric compounds amenable to the presentinvention includes oligonucleotide mimetics. The term mimetic as it isapplied to oligonucleotides is intended to include oligonucleotideswherein only the furanose ring or both the furanose ring and theinternucleotide linkage are replaced with novel groups, replacement ofonly the furanose ring is also referred to in the art as being a sugarsurrogate. The heterocyclic base moiety or a modified heterocyclic basemoiety is maintained for hybridization with an appropriate targetnucleic acid. One such oligonucleotide, an oligonucleotide mimetic thathas been shown to have excellent hybridization properties, is referredto as a peptide nucleic acid (PNA). In PNA oligonucleotides, thesugar-backbone of an oligonucleotide is replaced with an amidecontaining backbone, in particular an aminoethylglycine backbone. Thenucleobases are retained and are bound directly or indirectly to azanitrogen atoms of the amide portion of the backbone. RepresentativeUnited States patents that teach the preparation of PNA oligonucleotidesinclude, but are not limited to, U.S. Pat. Nos. 5,539,082; 5,714,331;and 5,719,262, each of which is herein incorporated by reference.Further teaching of PNA oligonucleotides can be found in Nielsen et al.,Science, 1991, 254, 1497-1500.

One oligonucleotide mimetic that has been reported to have excellenthybridization properties, is peptide nucleic acids (PNA). The backbonein PNA compounds is two or more linked aminoethylglycine units whichgives PNA an amide containing backbone. The heterocyclic base moietiesare bound directly or indirectly to aza nitrogen atoms of the amideportion of the backbone. Representative United States patents that teachthe preparation of PNA compounds include, but are not limited to, U.S.Pat. Nos. 5,539,082; 5,714,331; and 5,719,262, each of which is hereinincorporated by reference. Further teaching of PNA compounds can befound in Nielsen et al., Science, 1991, 254, 1497-1500.

Numerous modifications have been made to the structure of PNA since thebasic PNA structure was first prepared. The basic structure is shownbelow:

wherein

-   -   Bx is a heterocyclic base moiety;    -   T₄ is hydrogen, an amino protecting group, —C(O)R₅, substituted        or unsubstituted C₁-C₁₀ alkyl, substituted or unsubstituted        C₂-C₁₀ alkenyl, substituted or unsubstituted C₂-C₁₀ alkynyl,        alkylsulfonyl, arylsulfonyl, a chemical functional group, a        reporter group, a conjugate group, a D or L α-amino acid linked        via the α-carboxyl group or optionally through the ω-carboxyl        group when the amino acid is aspartic acid or glutamic acid or a        peptide derived from D, L or mixed D and L amino acids linked        through a carboxyl group, wherein the substituent groups are        selected from hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl,        nitro, thiol, thioalkoxy, halogen, alkyl, aryl, alkenyl and        alkynyl;    -   T₅ is —OH, —N(Z₁)Z₂, R₅, D or L α-amino acid linked via the        α-amino group or optionally through the ω-amino group when the        amino acid is lysine or ornithine or a peptide derived from D, L        or mixed D and L amino acids linked through an amino group, a        chemical functional group, a reporter group or a conjugate        group;    -   Z₁ is hydrogen, C₁-C₆ alkyl, or an amino protecting group;    -   Z₂ is hydrogen, C₁-C₆ alkyl, an amino protecting group,        —C(═O)—(CH₂)_(n)—J—Z₃, a D or L α-amino acid linked via the        a-carboxyl group or optionally through the co-carboxyl group        when the amino acid is aspartic acid or glutamic acid or a        peptide derived from D, L or mixed D and L amino acids linked        through a carboxyl group;    -   Z₃ is hydrogen, an amino protecting group, —C₁-C₆ alkyl,        —C(═O)—CH3, benzyl, benzoyl, or —(CH₂)_(n)—N(H)Z₁;    -   each J is O, S or NH;    -   R₅ is a carbonyl protecting group; and    -   n is from 2 to about 50.

Another class of oligonucleotide mimetic that has been studied is basedon linked morpholino units (morpholino nucleic acid) having heterocyclicbases attached to the morpholino ring. A number of linking groups havebeen reported that link the morpholino monomeric units in a morpholinonucleic acid. A preferred class of linking groups that have been used tolink morpholino monomeric units have also been used to give a non-ionicoligonucleotide. The non-ionic morpholino-based oligonucleotides areless likely to have undesired interactions with cellular proteins.Morpholino-based oligonucleotides are non-ionic mimics ofoligonucleotides and are less likely to form undesired interactions withcellular proteins (Dwaine A. Braasch and David R. Corey, Biochemistry,2002, 41(14), 4503-4510). Morpholino-based oligonucleotides aredisclosed in U.S. Pat. No. 5,034,506, issued Jul. 23, 1991. Themorpholino class of oligonucleotides have been prepared having a varietyof different linking groups joining the monomeric subunits.

Morpholino nucleic acids have been prepared having a variety ofdifferent linking groups (L₂) joining the monomeric subunits. The basicformula is shown below:

wherein

-   -   T₁ is hydroxyl or a protected hydroxyl;    -   T₅ is hydrogen or a phosphate or phosphate derivative;    -   L₂ is a linking group; and    -   n is from 2 to about 50.

A further class of oligonucleotide mimetic is referred to ascyclohexenyl nucleic acids (CeNA). The furanose ring normally present inan DNA/RNA molecule is replaced with a cyclohenyl ring. CeNA DMTprotected phosphoramidite monomers have been prepared and used foroligonucleotide synthesis following classical phosphoramidite chemistry.Fully modified CeNA oligonucleotides and oligonucleotides havingspecific positions modified with CeNA have been prepared and studied(see Wang et al., J. Am. Chem. Soc., 2000, 122, 8595-8602). In generalthe incorporation of CeNA monomers into a DNA chain increases itsstability of a DNA/RNA hybrid. CeNA oligoadenylates formed complexeswith RNA and DNA complements with similar stability to the nativecomplexes. The study of incorporating CeNA structures into naturalnucleic acid structures was shown by NMR and circular dichroism toproceed with easy conformational adaptation. Furthermore theincorporation of CeNA into a sequence targeting RNA was stable to serumand able to activate E. Coli RNase resulting in cleavage of the targetRNA strand.

The general formula of CeNA is shown below:

wherein

-   -   each Bx is a heterocyclic base moiety;    -   T₁ is hydroxyl or a protected hydroxyl; and    -   T₂ is hydroxyl or a protected hydroxyl.

Another class of oligonucleotide mimetic (anhydrohexitol nucleic acid)can be prepared from one or more anhydrohexitol nucleosides (see,Wouters and Herdewijn, Bioorg. Med. Chem. Lett., 1999, 9, 1563-1566) andwould have the general formula:

A further preferred modification includes Locked Nucleic Acids (LNAs) inwhich the 2′-hydroxyl group is linked to the 4′ carbon atom of the sugarring thereby forming a 2′-C,4′-C-oxymethylene linkage thereby forming abicyclic sugar moiety. The linkage is preferably a methylene (—CH₂—)_(n)group bridging the 2′ oxygen atom and the 4′ carbon atom wherein n is 1or 2 (Singh et al., Chem. Commun., 1998, 4, 455-456). LNA and LNAanalogs display very high duplex thermal stabilities with complementaryDNA and RNA (Tm=+3 to +10 C), stability towards 3′-exonucleolyticdegradation and good solubility properties. The basic structure of LNAshowing the bicyclic ring system is shown below:

The conformations of LNAs determined by 2D NMR spectroscopy have shownthat the locked orientation of the LNA nucleotides, both insingle-stranded LNA and in duplexes, constrains the phosphate backbonein such a way as to introduce a higher population of the N-typeconformation (Petersen et al., J. Mol. Recognit., 2000, 13, 44-53).These conformations are associated with improved stacking of thenucleobases (Wengel et al., Nucleosides Nucleotides, 1999, 18,1365-1370).

LNA has been shown to form exceedingly stable LNA:LNA duplexes (Koshkinet al., J. Am. Chem. Soc., 1998, 120, 13252-13253). LNA:LNAhybridization was shown to be the most thermally stable nucleic acidtype duplex system, and the RNA-mimicking character of LNA wasestablished at the duplex level. Introduction of 3 LNA monomers (T or A)significantly increased melting points (Tm=+15/+11) toward DNAcomplements. The universality of LNA-mediated hybridization has beenstressed by the formation of exceedingly stable LNA:LNA duplexes. TheRNA-mimicking of LNA was reflected with regard to the N-typeconformational restriction of the monomers and to the secondarystructure of the LNA:RNA duplex.

LNAs also form duplexes with complementary DNA, RNA or LNA with highthermal affinities. Circular dichroism (CD) spectra show that duplexesinvolving fully modified LNA (esp. LNA:RNA) structurally resemble anA-form RNA:RNA duplex. Nuclear magnetic resonance (NMR) examination ofan LNA:DNA duplex confirmed the 3′-endo conformation of an LNA monomer.Recognition of double-stranded DNA has also been demonstrated suggestingstrand invasion by LNA. Studies of mismatched sequences show that LNAsobey the Watson-Crick base pairing rules with generally improvedselectivity compared to the corresponding unmodified reference strands.

Novel types of LNA-oligonucleotides, as well as the LNAs, are useful ina wide range of diagnostic and therapeutic applications. Among these areantisense applications, PCR applications, strand-displacement oligomers,substrates for nucleic acid polymerases and generally as nucleotidebased drugs.

Potent and nontoxic antisense oligonucleotides containing LNAs have beendescribed (Wahlestedt et al., Proc. Natl. Acad. Sci. U.S.A., 2000, 97,5633-5638.) The authors have demonstrated that LNAs confer severaldesired properties to antisense agents. LNA/DNA copolymers were notdegraded readily in blood serum and cell extracts. LNA/DNA copolymersexhibited potent antisense activity in assay systems as disparate asG-protein-coupled receptor signaling in living rat brain and detectionof reporter genes in Escherichia coli. Lipofectin-mediated efficientdelivery of LNA into living human breast cancer cells has also beenaccomplished.

The synthesis and preparation of the LNA monomers adenine, cytosine,guanine, 5-methyl-cytosine, thymine and uracil, along with theiroligomerization, and nucleic acid recognition properties have beendescribed (Koshkin et al., Tetrahedron, 1998, 54, 3607-3630). LNAs andpreparation thereof are also described in WO 98/39352 and WO 99/14226.

The first analogs of LNA, phosphorothioate-LNA and 2′-thio-LNAs, havealso been prepared (Kumar et al., Bioorg. Med. Chem. Lett., 1998, 8,2219-2222). Preparation of locked nucleoside analogs containingoligodeoxyribonucleotide duplexes as substrates for nucleic acidpolymerases has also been described (Wengel et al., PCT InternationalApplication WO 98-DK393 19980914). Furthermore, synthesis of2′-amino-LNA, a novel conformationally restricted high-affinityoligonucleotide analog with a handle has been described in the art(Singh et al., J. Org. Chem., 1998, 63, 10035-10039). In addition,2′-Amino- and 2′-methylamino-LNA's have been prepared and the thermalstability of their duplexes with complementary RNA and DNA strands hasbeen previously reported.

Further oligonucleotide mimetics have been prepared to incude bicyclicand tricyclic nucleoside analogs having the formulas (amidite monomersshown):

(see Steffens et al., Hely. Chim. Acta, 1997, 80, 2426-2439; Steffens etal., J. Am. Chem. Soc., 1999, 121, 3249-3255; and Renneberg et al., J.Am. Chem. Soc., 2002, 124, 5993-6002). These modified nucleoside analogshave been oligomerized using the phosphoramidite approach and theresulting oligonucleotides containing tricyclic nucleoside analogs haveshown increased thermal stabilities (Tm's) when hybridized to DNA, RNAand itself. Oligonucleotides containing bicyclic nucleoside analogs haveshown thermal stabilities approaching that of DNA duplexes.

Another class of oligonucleotide mimetic is referred to asphosphonomonoester nucleic acids incorporate a phosphorus group in abackbone the backbone. This class of olignucleotide mimetic is reportedto have useful physical and biological and pharmacological properties inthe areas of inhibiting gene expression (antisense oligonucleotides,ribozymes, sense oligonucleotides and triplex-forming oligonucleotides),as probes for the detection of nucleic acids and as auxiliaries for usein molecular biology.

The general formula (for definitions of Markush variables see: U.S. Pat.Nos. 5,874,553 and 6,127,346 herein incorporated by reference in theirentirety) is shown below.

Another oligonucleotide mimetic has been reported wherein the furanosylring has been replaced by a cyclobutyl moiety.

Modified Internucleoside Linkages

Specific examples of preferred oligomeric compounds useful in thisinvention include oligonucleotides containing modified e.g.non-naturally occurring internucleoside linkages. As defined in thisspecification, oligonucleotides having modified internucleoside linkagesinclude internucleoside linkages that retain a phosphorus atom andinternucleoside linkages that do not have a phosphorus atom. For thepurposes of this specification, and as sometimes referenced in the art,modified oligonucleotides that do not have a phosphorus atom in theirinternucleoside backbone can also be considered to be oligonucleosides.

In the C. elegans system, modification of the internucleotide linkage(phosphorothioate) did not significantly interfere with RNAi activity.Based on this observation, it is suggested that certain preferredcompositions of the invention can also have one or more modifiedinternucleoside linkages. A preferred phosphorus containing modifiedinternucleoside linkage is the phosphorothioate internucleoside linkage.

Preferred modified oligonucleotide backbones containing a phosphorusatom therein include, for example, phosphorothioates, chiralphosphorothioates, phosphorodithioates, phosphotriesters,aminoalkylphosphotriesters, methyl and other alkyl phosphonatesincluding 3′-alkylene phosphonates, 5′-alkylene phosphonates and chiralphosphonates, phosphinates, phosphoramidates including 3′-aminophosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates,thionoalkylphosphonates, thionoalkylphosphotriesters, selenophosphatesand boranophosphates having normal 3′-5′ linkages, 2′-5′ linked analogsof these, and those having inverted polarity wherein one or moreinternucleotide linkages is a 3′ to 3′, 5′ to 5′ or 2′ to 2′ linkage.Preferred oligonucleotides having inverted polarity comprise a single 3′to 3′ linkage at the 3′-most internucleotide linkage i.e. a singleinverted nucleoside residue which may be abasic (the nucleobase ismissing or has a hydroxyl group in place thereof). Various salts, mixedsalts and free acid forms are also included.

Representative United States patents that teach the preparation of theabove phosphorus-containing linkages include, but are not limited to,U.S. Pat. Nos. 3,687,808; 4,469,863; 4,476,301; 5,023,243; 5,177,196;5,188,897; 5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131;5,399,676; 5,405,939; 5,453,496; 5,455,233; 5,466,677; 5,476,925;5,519,126; 5,536,821; 5,541,306; 5,550,111; 5,563,253; 5,571,799;5,587,361; 5,194,599; 5,565,555; 5,527,899; 5,721,218; 5,672,697 and5,625,050, certain of which are commonly owned with this application,and each of which is herein incorporated by reference.

In more preferred embodiments of the invention, oligonucleotides haveone or more phosphorothioate and/or heteroatom internucleoside linkages,in particular —CH₂—NH—O—CH₂—, —CH₂—N(CH₃)—O—CH₂— [known as a methylene(methylimino) or MMI backbone], —CH₂—O—N(CH₃)—CH₂—,—CH₂—N(CH₃)—N(CH₃)—CH₂— and —O—N(CH₃)—CH₂—CH₂— [wherein the nativephosphodiester internucleotide linkage is represented as—O—P(═O)(OH)—O—CH₂—]. The MMI type internucleoside linkages aredisclosed in the above referenced U.S. Pat. No. 5,489,677. Preferredamide internucleoside linkages are disclosed in the above referencedU.S. Pat. No. 5,602,240.

Preferred modified oligonucleotide backbones that do not include aphosphorus atom therein have backbones that are formed by short chainalkyl or cycloalkyl internucleoside linkages, mixed heteroatom and alkylor cycloalkyl internucleoside linkages, or one or more short chainheteroatomic or heterocyclic internucleoside linkages. These includethose having morpholino linkages (formed in part from the sugar portionof a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfonebackbones; formacetyl and thioformacetyl backbones; methylene formacetyland thioformacetyl backbones; riboacetyl backbones; alkene containingbackbones; sulfamate backbones; methyleneimino and methylenehydrazinobackbones; sulfonate and sulfonamide backbones; amide backbones; andothers having mixed N, O, S and CH₂ component parts.

Representative United States patents that teach the preparation of theabove oligonucleosides include, but are not limited to, U.S. Pat. Nos.5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141; 5,235,033;5,264,562; 5,264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967;5,489,677; 5,541,307; 5,561,225; 5,596,086; 5,602,240; 5,610,289;5,602,240; 5,608,046; 5,610,289; 5,618,704; 5,623,070; 5,663,312;5,633,360; 5,677,437; 5,792,608; 5,646,269 and 5,677,439, certain ofwhich are commonly owned with this application, and each of which isherein incorporated by reference.

Modified Sugars

In addition to having at least one alternating motif the compositions ofthe present invention may also contain additional modified sugarmoieties. Preferred modified sugar moieties comprise a sugar substituentgroup, which is normally attached to the 2′-position but alternativelycan be attached to the 3′, 4′ or 5′-position, selected from: OH; F; O—,S—, or N-alkyl; O—, S—, or N-alkenyl; O—, S— or N-alkynyl; orO-alkyl-O-alkyl, wherein the alkyl, alkenyl and alkynyl may besubstituted or unsubstituted C₁ to C₁₀ alkyl or C₂ to C₁₀ alkenyl andalkynyl. Particularly preferred are O[(CH₂)_(n)O]_(m)CH₃, O(CH₂)_(n)OCH₃, O(CH₂)_(n)NH₂, O(CH₂)_(n)CH₃, O(CH₂)_(n)ONH₂, andO(CH₂)_(n)ON—[(CH₂)_(n)CH₃]₂, where n and m are from 1 to about 10.Other preferred sugar substituent groups include: C₁ to C₁₀ lower alkyl,substituted lower alkyl, alkenyl, alkynyl, alkaryl, aralkyl, O-alkarylor O-aralkyl, SH, SCH₃, OCN, Cl, Br, CN, CF₃, OCF₃, SOCH₃, SO₂CH₃, ONO₂,NO₂, N₃, NH₂, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino,polyalkylamino, substituted silyl, an RNA cleaving group, a reportergroup, an intercalator, a group for improving the pharmacokineticproperties of an oligonucleotide, or a group for improving thepharmacodynamic properties of an oligonucleotide, and other substituentshaving similar properties. A preferred modification includes2′-methoxyethoxy (2′-O—CH₂CH₂OCH₃, also known as 2′-O-(2-methoxyethyl)or 2′-MOE) (Martin et al., Helv. Chim. Acta, 1995, 78, 486-504) i.e., analkoxyalkoxy group. A further preferred modification includes2′-dimethylaminooxyethoxy, i.e., O(CH₂)₂ON(CH₃)₂ group, also known as2′-DMAOE, as described in examples hereinbelow, and2′-dimethylaminoethoxyethoxy (also known in the art as2′-O-dimethyl-amino-ethoxy-ethyl or 2′-DMAEOE), i.e.,2′-O-CH2OCH₂N(CH₃)₂.

Other preferred sugar substituent groups include methoxy (—O—CH₃),aminopropoxy (—OCH₂CH₂CH₂NH₂), allyl (—CH₂—CH═CH₂), —O-allyl(—O—CH₂—CH═CH₂) and fluoro (F). 2′-Sugar substituent groups may be inthe arabino (up) position or ribo (down) position. A preferred2′-arabino modification is 2′-F. Similar modifications may also be madeat other positions on the oligomeric compoiund, particularly the 3′position of the sugar on the 3′ terminal nucleoside or in 2′-5′ linkedoligonucleotides and the 5′ position of 5′ terminal nucleotide.Oligonucleotides may also have sugar mimetics such as cyclobutylmoieties in place of the pentofuranosyl sugar. Representative UnitedStates patents that teach the preparation of such modified sugarstructures include, but are not limited to, U.S. Pat. Nos. 4,981,957;5,118,800; 5,319,080; 5,359,044; 5,393,878; 5,446,137; 5,466,786;5,514,785; 5,519,134; 5,567,811; 5,576,427; 5,591,722; 5,597,909;5,610,300; 5,627,053; 5,639,873; 5,646,265; 5,658,873; 5,670,633;5,792,747; and 5,700,920, certain of which are commonly owned with theinstant application, and each of which is herein incorporated byreference in its entirety.

Further representative sugar substituent groups include groups offormula I_(a) or II_(a):

wherein:

-   -   R_(b) is O, S or NH;    -   R_(d) is a single bond, O, S or C(═O);    -   R_(e) is C₁-C₁₀ alkyl, N(R_(k))(R_(m)), N(R_(k))(R_(n)),        N═C(R_(p))(R_(q)), N═C(R_(p))(R_(r)) or has formula III_(a);

-   -   R_(p) and R_(q) are each independently hydrogen or C₁-C₁₀ alkyl;    -   R_(r) is —R_(x)—R_(y);    -   each R_(s), R_(t), R_(u) and R_(v) is, independently, hydrogen,        C(O)R_(w), substituted or unsubstituted C₁-C₁₀ alkyl,        substituted or unsubstituted C₂-C₁₀ to alkenyl, substituted or        unsubstituted C₂-C₁₀ alkynyl, alkylsulfonyl, arylsulfonyl, a        chemical functional group or a conjugate group, wherein the        substituent groups are selected from hydroxyl, amino, alkoxy,        carboxy, benzyl, phenyl, nitro, thiol, thioalkoxy, halogen,        alkyl, aryl, alkenyl and alkynyl;    -   or optionally, R_(u) and R_(v), together form a phthalimido        moiety with the nitrogen atom to which they are attached;    -   each R_(w) is, independently, substituted or unsubstituted        C₁-C₁₀ alkyl, trifluoromethyl, cyanoethyloxy, methoxy, ethoxy,        t-butoxy, allyloxy, 9-fluorenylmethoxy,        2-(trimethylsilyl)-ethoxy, 2,2,2-trichloroethoxy, benzyloxy,        butyryl, iso-butyryl, phenyl or aryl;    -   R_(k) is hydrogen, a nitrogen protecting group or —R_(x)—R_(y);    -   R_(p) is hydrogen, a nitrogen protecting group or —R_(x)—R_(y);    -   R_(x) is a bond or a linking moiety;    -   R_(y) is a chemical functional group, a conjugate group or a        solid support medium;    -   each R_(m) and R_(n) is, independently, H, a nitrogen protecting        group, substituted or unsubstituted C₁-C₁₀ alkyl, substituted or        unsubstituted C₂-C₁₀ to alkenyl, substituted or unsubstituted        C₂-C₁₀ alkynyl, wherein the substituent groups are selected from        hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro, thiol,        thioalkoxy, halogen, alkyl, aryl, alkenyl, alkynyl; NH₃ ⁺,        N(R_(u))(R_(v)), guanidino and acyl where said acyl is an acid        amide or an ester;    -   or R_(m) and R_(n), together, are a nitrogen protecting group,        are joined in a ring structure that optionally includes an        additional heteroatom selected from N and O or are a chemical        functional group;    -   R_(i) is OR_(z), SR_(z), or N(R_(z))₂;    -   each R_(z) is, independently, H, C₁-C₈ alkyl, C₁-C₈ haloalkyl,        C(═NH)N(H)R_(u), C(═O)N(H)R_(u) or OC(═O)N(H)R,_(u);    -   R_(f), R_(g) and R_(h) comprise a ring system having from about        4 to about 7 carbon atoms or having from about 3 to about 6        carbon atoms and 1 or 2 heteroatoms wherein said heteroatoms are        selected from oxygen, nitrogen and sulfur and wherein said ring        system is aliphatic, unsaturated aliphatic, aromatic, or        saturated or unsaturated heterocyclic;    -   R_(j) is alkyl or haloalkyl having 1 to about 10 carbon atoms,        alkenyl having 2 to about 10 carbon atoms, alkynyl having 2 to        about 10 carbon atoms, aryl having 6 to about 14 carbon atoms,        N(R_(k))(R_(m)) OR_(k), halo, SR_(k) or CN;    -   m_(a) is 1 to about 10;    -   each mb is, independently, 0 or 1;    -   mc is 0 or an integer from 1 to 10;    -   md is an integer from 1 to 10;    -   me is from 0, 1 or 2; and    -   provided that when mc is 0, md is greater than 1.

Representative substituents groups of Formula I are disclosed in U.S.patent application Ser. No. 09/130,973, filed Aug. 7, 1998, entitled“Capped 2′-Oxyethoxy Oligonucleotides,” hereby incorporated by referencein its entirety.

Representative cyclic substituent groups of Formula II are disclosed inU.S. patent application Ser. No. 09/123,108, filed Jul. 27, 1998,entitled “RNA Targeted 2′-Oligonucleotides that are ConformationallyPreorganized,” hereby incorporated by reference in its entirety.

Particularly preferred sugar substituent groups includeO[(CH₂)_(n)O]_(m)CH_(3,)O(CH₂)_(n)OCH₃, O(CH₂)_(n)NH₂, O(CH₂)_(n)CH₃,O(CH₂)_(n)ONH₂, and O(CH₂)_(n)ON[(CH₂)_(n)CH₃)]₂, where n and m are from1 to about 10.

Representative guanidino substituent groups that are shown in formulaIII and IV are disclosed in co-owned U.S patent application Ser. No.09/349,040, entitled “Functionalized Oligomers”, filed Jul. 7, 1999,hereby incorporated by reference in its entirety.

Representative acetamido substituent groups are disclosed in U.S. Pat.No. 6,147,200 which is hereby incorporated by reference in its entirety.

Representative dimethylaminoethyloxyethyl substituent groups aredisclosed in International Patent Application PCT/US99/17895, entitled“2′-O-Dimethyl aminoethyloxyethyl-Oligonucleotides”, filed Aug. 6, 1999,hereby incorporated by reference in its entirety.

Modified Nucleobases/Naturally Occurring Nucleobases

Oligomeric compounds may also include nucleosides or other surrogate ormimetic monomeric subunits that include a nucleobase (often referred toin the art simply as “base” or “heterocyclic base moiety”). Thenucleobase is another moiety that has been extensively modified orsubstituted and such modified and or substituted nucleobases areamenable to the present invention. As used herein, “unmodified” or“natural” nucleobases include the purine bases adenine (A) and guanine(G), and the pyrimidine bases thymine (T), cytosine (C) and uracil (U).Modified nucleobases also referred herein as heterocyclic base moietiesinclude other synthetic and natural nucleobases such as 5-methylcytosine(5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine,2-aminoadenine, 6-methyl and other alkyl derivatives of adenine andguanine, 2-propyl and other alkyl derivatives of adenine and guanine,2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil andcytosine, 5-propynyl (—C≡C—CH₃) uracil and cytosine and other alkynylderivatives of pyrimidine bases, 6-azo uracil, cytosine and thymine,5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol,8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines,5-halo particularly 5-bromo, 5-trifluoromethyl and other 5-substituteduracils and cytosines, 7-methylguanine and 7-methyladenine, 2-F-adenine,2-amino-adenine, 8-azaguanine and 8-azaadenine, 7-deazaguanine and7-deazaadenine and 3-deazaguanine and 3-deazaadenine.

Nucleobases may also include those in which the purine or pyrimidinebase is replaced with other heterocycles, for example 7-deaza-adenine,7-deazaguanosine, 2-aminopyridine and 2-pyridone. Further nucleobasesinclude those disclosed in U.S. Pat. No. 3,687,808, those disclosed inThe Concise Encyclopedia Of Polymer Science And Engineering, pages858-859, Kroschwitz, J. I., ed. John Wiley & Sons, 1990, those disclosedby Englisch et al., Angewandte Chemie, International Edition, 1991, 30,613, and those disclosed by Sanghvi, Y. S., Chapter 15, AntisenseResearch and Applications, pages 289-302, Crooke, S. T. and Lebleu, B. ,ed., CRC Press, 1993. Certain of these nucleobases are particularlyuseful for increasing the binding affinity of the compositions of theinvention. These include 5- substituted pyrimidines, 6-azapyrimidinesand N-2, N-6 and 0-6 substituted purines, including 2aminopropyladenine, 5-propynyluracil and 5-propynylcytosine. 5methylcytosine substitutions have been shown to increase nucleic acidduplex stability by 0.6-1.2° C. (Sanghvi, Y. S., Crooke, S. T. andLebleu, B., eds., Antisense Research and Applications, CRC Press, BocaRaton, 1993, pp. 276-278) and are presently preferred basesubstitutions, even more particularly when combined with2′-O-methoxyethyl sugar modifications.

Oligomeric compounds of the present invention can also includepolycyclic heterocyclic compounds in place of one or more heterocyclicbase moieties. A number of tricyclic heterocyclic comounds have beenpreviously reported. These compounds are routinely used in antisenseapplications to increase the binding properties of the modified strandto a target strand. The most studied modifications are targeted toguanosines hence they have been termed G-clamps or cytidine analogs.Many of these polycyclic heterocyclic compounds have the generalformula:

Representative cytosine analogs that make 3 hydrogen bonds with aguanosine in a second strand include 1,3-diazaphenoxazine-2-one (R₁₀=O,R₁₁-R₁₄=H) [Kurchavov, et al., Nucleosides and Nucleotides, 1997, 16,1837-1846], 1,3-diazaphenothiazine-2-one (R₁₀=S, R₁₁-R₁₄=H), [Lin,K.-Y.; Jones, R. J.; Matteucci, M. J. Am. Chem. Soc. 1995, 117,3873-3874] and 6,7,8,9-tetrafluoro-1,3-diazaphenoxazine-2-one (R₁₀=O,R₁₁- R₁₄=F) [Wang, J.; Lin, K.-Y., Matteucci, M. Tetrahedron Lett. 1998,39, 8385-8388]. Incorporated into oligonucleotides these basemodifications were shown to hybridize with complementary guanine and thelatter was also shown to hybridize with adenine and to enhance helicalthermal stability by extended stacking interactions(also see U.S. PatentApplication entitled “Modified Peptide Nucleic Acids” filed May 24,2002, Ser. No. 10/155,920; and U.S. Patent Application entitled“Nuclease Resistant Chimeric Oligonucleotides” filed May 24, 2002, Ser.No. 10/013,295, both of which are commonly owned with this applicationand are herein incorporated by reference in their entirety).

Further helix-stabilizing properties have been observed when a cytosineanalog/substitute has an aminoethoxy moiety attached to the rigid1,3-diazaphenoxazine-2-one scaffold (R₁₀=O, R₁₁=—O—(CH₂)₂—NH₂, R₁₂₋₁₄=H)[Lin, K.-Y.; Matteucci, M. J. Am. Chem. Soc. 1998, 120, 8531-8532].Binding studies demonstrated that a single incorporation could enhancethe binding affinity of a model oligonucleotide to its complementarytarget DNA or RNA with a ΔT_(m) of up to 18° relative to 5-methylcytosine (dC5^(me)), which is the highest known affinity enhancement fora single modification, yet. On the other hand, the gain in helicalstability does not compromise the specificity of the oligonucleotides.The T_(m) data indicate an even greater discrimination between theperfect match and mismatched sequences compared to dC5^(me). It wassuggested that the tethered amino group serves as an additional hydrogenbond donor to interact with the Hoogsteen face, namely the O6, of acomplementary guanine thereby forming 4 hydrogen bonds. This means thatthe increased affinity of G-clamp is mediated by the combination ofextended base stacking and additional specific hydrogen bonding.

Further tricyclic heterocyclic compounds and methods of using them thatare amenable to the present invention are disclosed in U.S. Pat. No.6,028,183, which issued on May 22, 2000, and U.S. Pat. No. 6,007,992,which issued on Dec. 28, 1999, the contents of both are commonlyassigned with this application and are incorporated herein in theirentirety.

The enhanced binding affinity of the phenoxazine derivatives togetherwith their uncompromised sequence specificity makes them valuablenucleobase analogs for the development of more potent antisense-baseddrugs. In fact, promising data have been derived from in vitroexperiments demonstrating that heptanucleotides containing phenoxazinesubstitutions are capable to activate RNaseH, enhance cellular uptakeand exhibit an increased antisense activity [Lin, K-Y; Matteucci, M. J.Am. Chem. Soc. 1998, 120, 8531-8532]. The activity enhancement was evenmore pronounced in case of G-clamp, as a single substitution was shownto significantly improve the in vitro potency of a 20mer2′-deoxyphosphorothioate oligonucleotides [Flanagan, W. M.; Wolf, J. J.;Olson, P.; Grant, D.; Lin, K.-Y.; Wagner, R. W.; Matteucci, M. Proc.Natl. Acad. Sci. USA, 1999, 96, 3513-3518]. Nevertheless, to optimizeoligonucleotide design and to better understand the impact of theseheterocyclic modifications on the biological activity, it is importantto evaluate their effect on the nuclease stability of the oligomers.

Further modified polycyclic heterocyclic compounds useful as nucleobasesare disclosed in but not limited to, the above noted U.S. Pat. No.3,687,808, as well as U.S. Pat. Nos. 4,845,205; 5,130,302; 5,134,066;5,175,273; 5,367,066; 5,432,272; 5,434,257; 5,457,187; 5,459,255;5,484,908; 5,502,177; 5,525,711; 5,552,540; 5,587,469; 5,594,121,5,596,091; 5,614,617; 5,645,985; 5,646,269; 5,750,692; 5,830,653;5,763,588; 6,005,096; and 5,681,941, and U.S. patent application Ser.No. 09/996,292 filed Nov. 28, 2001, certain of which are commonly ownedwith the instant application, and each of which is herein incorporatedby reference.

Conjugates

Oligomeric compounds used in the compositions of the present inventioncan also be modified to have one or more moieties or conjugates whichenhance their activity, cellular distribution or cellular uptake. In oneembodiment such modified oligomeric compounds are prepared by covalentlyattaching conjugate groups to functional groups such as hydroxyl oramino groups. Conjugate groups of the invention include intercalators,reporter molecules, polyamines, polyamides, polyethylene glycols,polyethers, groups that enhance the pharmacodynamic properties ofoligomers, and groups that enhance the pharmacokinetic properties ofoligomers. Typical conjugates groups include cholesterols, lipids,phospholipids, biotin, phenazine, folate, phenanthridine, anthraquinone,acridine, fluoresceins, rhodamines, coumarins, and dyes. Groups thatenhance the pharmacodynamic properties, in the context of thisinvention, include groups that improve oligomer uptake, enhance oligomerresistance to degradation, and/or strengthen sequence-specifichybridization with RNA. Groups that enhance the pharmacokineticproperties, in the context of this invention, include groups thatimprove oligomer uptake, distribution, metabolism or excretion.Representative conjugate groups are disclosed in International PatentApplication PCT/US92/09196, filed Oct. 23, 1992 the entire disclosure ofwhich is incorporated herein by reference. Conjugate moieties includebut are not limited to lipid moieties such as a cholesterol moiety(Letsinger et al., Proc. Natl. Acad. Sci. USA, 1989, 86, 6553-6556),cholic acid (Manoharan et al., Bioorg. Med. Chem. Let., 1994, 4,1053-1060), a thioether, e.g., hexyl-S-tritylthiol (Manoharan et al.,Ann. N.Y. Acad. Sci., 1992, 660, 306-309; Manoharan et al., Bioorg. Med.Chem. Let., 1993, 3, 2765-2770), a thiocholesterol (Oberhauser et al.,Nucl. Acids Res., 1992, 20, 533-538), an aliphatic chain, e.g.,dodecandiol or undecyl residues (Saison-Behmoaras et al., EMBOI, 1991,10, 1111-1118; Kabanov et al., FEBS Lett., 1990, 259, 327-330;Svinarchuk et al., Biochimie, 1993, 75, 49-54), a phospholipid, e.g.,di-hexadecyl-rac-glycerol or triethylammonium1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate (Manoharan et al.,Tetrahedron Lett., 1995, 36, 3651-3654; Shea et al., Nucl. Acids Res.,1990, 18, 3777-3783), a polyamine or a polyethylene glycol chain(Manoharan et al., Nucleosides & Nucleotides, 1995, 14, 969-973), oradamantane acetic acid (Manoharan et al., Tetrahedron Lett., 1995, 36,3651-3654), a palmityl moiety (Mishra et al., Biochim. Biophys. Acta,1995, 1264, 229-237), or an octadecylamine orhexylamino-carbonyl-oxycholesterol moiety (Crooke et al., J. Pharmacol.Exp. Ther., 1996, 277, 923-937.

The compositions of the invention may also be conjugated to active drugsubstances, for example, aspirin, warfarin, phenylbutazone, ibuprofen,suprofen, fenbufen, ketoprofen, (S)-(+)-pranoprofen, carprofen,dansylsarcosine, 2,3,5-triiodobenzoic acid, flufenamic acid, folinicacid, a benzothiadiazide, chlorothiazide, a diazepine, indomethicin, abarbiturate, a cephalosporin, a sulfa drug, an antidiabetic, anantibacterial or an antibiotic. Oligonucleotide-drug conjugates andtheir preparation are described in U.S. patent application Ser. No09/334,130 (filed Jun. 15, 1999), incorporated herein by reference inits entirety.

Representative United States patents that teach the preparation of sucholigonucleotide conjugates include, but are not limited to, U.S. Pat.Nos. 4,828,979; 4,948,882; 5,218,105; 5,525,465; 5,541,313; 5,545,730;5,552,538; 5,578,717, 5,580,731; 5,580,731; 5,591,584; 5,109,124;5,118,802; 5,138,045; 5,414,077; 5,486,603; 5,512,439; 5,578,718;5,608,046; 4,587,044; 4,605,735; 4,667,025; 4,762,779; 4,789,737;4,824,941; 4,835,263; 4,876,335; 4,904,582; 4,958,013; 5,082,830;5,112,963; 5,214,136; 5,082,830; 5,112,963; 5,214,136; 5,245,022;5,254,469; 5,258,506; 5,262,536; 5,272,250; 5,292,873; 5,317,098;5,371,241, 5,391,723; 5,416,203, 5,451,463; 5,510,475; 5,512,667;5,514,785; 5,565,552; 5,567,810; 5,574,142; 5,585,481; 5,587,371;5,595,726; 5,597,696; 5,599,923; 5,599,928 and 5,688,941, certain ofwhich are commonly owned with the instant application, and each of whichis herein incorporated by reference.

Oligomeric compounds used in the compositions of the present inventioncan also be modified to have one or more stabilizing groups that aregenerally attached to one or both termini of oligomeric compounds toenhance properties such as for example nuclease stability. Included instabilizing groups are cap structures. By “cap structure or terminal capmoiety” is meant chemical modifications, which have been incorporated ateither terminus of oligonucleotides (see for example Wincott et al., WO97/26270, incorporated by reference herein). These terminalmodifications protect the oligomeric compounds having terminal nucleicacid molecules from exonuclease degradation, and can help in deliveryand/or localization within a cell. The cap can be present at the5′-terminus (5′-cap) or at the 3′-terminus (3′-cap) or can be present onboth termini. In non-limiting examples, the 5′-cap includes invertedabasic residue (moiety), 4′,5′-methylene nucleotide;1-(beta-D-erythrofuranosyl) nucleotide, 4′-thio nucleotide, carbocyclicnucleotide; 1,5-anhydrohexitol nucleotide; L-nucleotides;alpha-nucleotides; modified base nucleotide; phosphorodithioate linkage;threo-pentofuranosyl nucleotide; acyclic 3′,4′-seco nucleotide; acyclic3,4-dihydroxybutyl nucleotide; acyclic 3,5-dihydroxypentyl riucleotide,3′-3′-inverted nucleotide moiety; 3′-3′-inverted abasic moiety;3′-2′-inverted nucleotide moiety; 3′-2′-inverted abasic moiety;1,4-butanediol phosphate; 3′-phosphoramidate; hexylphosphate; aminohexylphosphate; 3′-phosphate; 3′-phosphorothioate; phosphorodithioate; orbridging or non-bridging methylphosphonate moiety (for more details seeWincott et al., International PCT publication No. WO 97/26270,incorporated by reference herein).

Particularly preferred 3′-cap structures of the present inventioninclude, for example 4′,5′-methylene nucleotide;1-(beta-D-erythrofuranosyl) nucleotide; 4′-thio nucleotide, carbocyclicnucleotide; 5′-amino-alkyl phosphate; 1,3-diamino-2-propyl phosphate,3-aminopropyl phosphate; 6-aminohexyl phosphate; 1,2-aminododecylphosphate; hydroxypropyl phosphate; 1,5-anhydrohexitol nucleotide;L-nucleotide; alpha-nucleotide; modified base nucleotide;phosphorodithioate; threo-pentofuranosyl nucleotide; acyclic 3′,4′-seconucleotide; 3,4-dihydroxybutyl nucleotide; 3,5-dihydroxypentylnucleotide, 5′-5′-inverted nucleotide moiety; 5′-5′-inverted abasicmoiety; 5′-phosphoramidate; 5′-phosphorothioate; 1,4-butanediolphosphate; 5′-amino; bridging and/or non-bridging 5′-phosphoramidate,phosphorothioate and/or phosphorodithioate, bridging or non bridgingmethylphosphonate and 5′-mercapto moieties (for more details seeBeaucage and Tyer, 1993, Tetrahedron 49, 1925; incorporated by referenceherein).

3′-Endo Modifications

In one aspect of the present invention oligomeric compounds includenucleosides that are chemically modified to induce a 3′-endo sugarconformation. A nucleoside can have a chemical modification of thenucleobase, the sugar moiety or both to induce a 3′-endo sugarconformation. These modified nucleosides are used to mimic RNA likenucleosides so that particular properties of an oligomeric compoundespecially an oligonucleotide can be enhanced while maintaining thedesirable 3′-endo conformational geometry. There is an apparentpreference for an RNA type duplex (A form helix, predominantly 3′-endo)as a requirement of RNA interference which is supported in part by thefact that duplexes composed of 2′-deoxy-2′-F-nucleosides appearefficient in triggering RNAi response in the C. elegans system.Properties that are enhanced by using more stable 3′-endo nucleosidesinclude but aren't limited to modulation of pharmacokinetic propertiesthrough modification of protein binding, protein off-rate, absorptionand clearance; modulation of nuclease stability as well as chemicalstability; modulation of the binding affinity and specificity of theoligomer (affinity and specificity for enzymes as well as forcomplementary sequences); and increasing efficacy of RNA cleavage. Thepresent invention includes oligomeric compounds having at least one2′-O-methyl modified nucleoside and further comprising additionalnucleosides that are modified in such a way as to favor a C3′-endo typeconformation.

Nucleoside conformation is influenced by various factors includingsubstitution at the 2′,3′ or 4′-positions of the pentofuranosyl sugar.Electronegative substituents generally prefer the axial positions, whilesterically demanding substituents generally prefer the equatorialpositions (Principles of Nucleic Acid Structure, Wolfgang Sanger, 1984,Springer-Verlag.) Modification of the 2′ position to favor the 3′-endoconformation can be achieved while maintaining the 2′-OH as arecognition element, as illustrated in FIG. 2, below (Gallo et al.,Tetrahedron (2001), 57, 5707-5713. Harry-O′kuru et al., J. Org. Chem.,(1997), 62(6), 1754-1759 and Tang et al., J. Org. Chem. (1999), 64,747-754.) Alternatively, preference for the 3′-endo conformation can beachieved by deletion of the 2′-OH as exemplified by2′deoxy-2′F-nucleosides (Kawasaki et al., J. Med. Chem. (1993), 36,831-841), which adopts the 3′-endo conformation positioning theelectronegative fluorine atom in the axial position. Other modificationsof the ribose ring, for example substitution at the 4′-position to give4′-F modified nucleosides (Guillerm et al., Bioorganic and MedicinalChemistry Letters (1995), 5, 1455-1460 and Owen et al., J. Org. Chem.(1976), 41, 3010-3017), or for example modification to yieldmethanocarba nucleoside analogs (Jacobson et al., J. Med. Chem. Lett.(2000), 43, 2196-2203 and Lee et al., Bioorganic and Medicinal ChemistryLetters (2001), 11, 1333-1337) also induce preference for the 3′-endoconformation. Some modifications actually lock the conformationalgeometry by formation of a bicyclic sugar moiety e.g. locked nucleicacid (LNA, Singh et al, Chem. Commun. (1998), 4, 455-456), and ethylenebridged nucleic acids (ENA, Morita et al, Bioorganic & MedicinalChemistry Letters (2002), 12, 73-76.)

Examples of modified nucleosides amenable to the present invention areshown below in Table I. These examples are meant to be representativeand not exhaustive.

TABLE I

The preferred conformation of modified nucleosides and their oligomerscan be estimated by various methods such as molecular dynamicscalculations, nuclear magnetic resonance spectroscopy and CDmeasurements. Hence, modifications predicted to induce RNA likeconformations, A-form duplex geometry in an oligomeric context, areselected for use in one or more of the oligonucleotides of the presentinvention. The synthesis of numerous of the modified nucleosidesamenable to the present invention are known in the art (see for example,Chemistry of Nucleosides and Nucleotides Vol 1-3, ed. Leroy B. Townsend,1988, Plenum press., and the examples section below.) Nucleosides knownto be inhibitors/substrates for RNA dependent RNA polymerases (forexample HCV NS5B

In one aspect, the present invention is directed to oligonucleotidesthat are prepared having enhanced properties compared to native RNAagainst nucleic acid targets. A target is identified and anoligonucleotide is selected having an effective length and sequence thatis complementary to a portion of the target sequence. Each nucleoside ofthe selected sequence is scrutinized for possible enhancingmodifications. A preferred modification would be the replacement of oneor more RNA nucleosides with nucleosides that have the same 3′-endoconformational geometry. Such modifications can enhance chemical andnuclease stability relative to native RNA while at the same time beingmuch cheaper and easier to synthesize and/or incorporate into anoligonucleotide. The selected sequence can be further divided intoregions and the nucleosides of each region evaluated for enhancingmodifications that can be the result of a chimeric configuration.Consideration is also given to the termini (e.g. 5′ and 3′-termini) asthere are often advantageous modifications that can be made to one ormore of the terminal monomeric subunits. In one aspect of the invention,desired properties and or activity of oligonucleotides are enhanced bythe inclusion of a 5′-phosphate or modified phosphate moiety.

The terms used to describe the conformational geometry of homoduplexnucleic acids are “A Form” for RNA and “B Form” for DNA. The respectiveconformational geometry for RNA and DNA duplexes was determined fromX-ray diffraction analysis of nucleic acid fibers (Arnott and Hukins,Biochem. Biophys. Res. Comm., 1970, 47, 1504.) In general, RNA:RNAduplexes are more stable and have higher melting temperatures (Tm's)than DNA:DNA duplexes (Sanger et al., Principles of Nucleic AcidStructure, 1984, Springer-Verlag; New York, N.Y.; Lesnik et al.,Biochemistry, 1995, 34, 10807-10815; Conte et al., Nucleic Acids Res.,1997, 25, 2627-2634). The increased stability of RNA has been attributedto several structural features, most notably the improved base stackinginteractions that result from an A-form geometry (Searle et al., NucleicAcids Res., 1993, 21, 2051-2056). The presence of the 2′ hydroxyl in RNAbiases the sugar toward a C3′ endo pucker, i.e., also designated asNorthern pucker, which causes the duplex to favor the A-form geometry.In addition, the 2′ hydroxyl groups of RNA can form a network of watermediated hydrogen bonds that help stabilize the RNA duplex (Egli et al.,Biochemistry, 1996, 35, 8489-8494). On the other hand, deoxy nucleicacids prefer a C2′ endo sugar pucker, i.e., also known as Southernpucker, which is thought to impart a less stable B-form geometry(Sanger, W. (1984) Principles of Nucleic Acid Structure,Springer-Verlag, New York, N.Y.). As used herein, B-form geometry isinclusive of both C2′-endo pucker and 04′-endo pucker. This isconsistent with Berger, et. al., Nucleic Acids Research, 1998, 26,2473-2480, who pointed out that in considering the furanoseconformations which give rise to B-form duplexes consideration shouldalso be given to a O4′-endo pucker contribution.

DNA:RNA hybrid duplexes, however, are usually less stable than pureRNA:RNA duplexes, and depending on their sequence may be either more orless stable than DNA:DNA duplexes (Searle et al., Nucleic Acids Res.,1993, 21, 2051-2056). The structure of a hybrid duplex is intermediatebetween A- and B-form geometries, which may result in poor stackinginteractions (Lane et al., Eur. J. Biochem., 1993, 215, 297-306;Fedoroff et al., J. Mol. Biol., 1993, 233, 509-523; Gonzalez et al.,Biochemistry, 1995, 34, 4969-4982; Horton et al., J. Mol. Biol., 1996,264, 521-533). The stability of the duplex formed between a target RNAand a synthetic sequence is central to therapies such as but not limitedto antisense and RNA interference as these mechanisms require thebinding of a synthetic strand of oligonucleotide to an RNA targetstrand. In the case of antisense, effective inhibition of the mRNArequires that the antisense DNA have a very high binding affinity withthe mRNA. Otherwise the desired interaction between the synthetic strandand target mRNA strand will occur infrequently, resulting in decreasedefficacy.

One routinely used method of modifying the sugar puckering is thesubstitution of the sugar at the 2′-position with a substituent groupthat influences the sugar geometry. The influence on ring conformationis dependant on the nature of the substituent at the 2′-position. Anumber of different substituents have been studied to determine theirsugar puckering effect. For example, 2′-halogens have been studiedshowing that the 2′-fluoro derivative exhibits the largest population(65%) of the C3′-endo form, and the 2′-iodo exhibits the lowestpopulation (7%). The populations of adenosine (2′-OH) versusdeoxyadenosine (2′-H) are 36% and 19%, respectively. Furthermore, theeffect of the 2′-fluoro group of adenosine dimers(2′-deoxy-2′-fluoroadenosine -2′-deoxy-2′-fluoro-adenosine) is furthercorrelated to the stabilization of the stacked conformation.

As expected, the relative duplex stability can be enhanced byreplacement of 2′-OH groups with 2′-F groups thereby increasing theC3′-endo population. It is assumed that the highly polar nature of the2′-F bond and the extreme preference for C3′-endo puckering maystabilize the stacked conformation in an A-form duplex. Data from UVhypochromicity, circular dichroism, and ¹H NMR also indicate that thedegree of stacking decreases as the electronegativity of the halosubstituent decreases. Furthermore, steric bulk at the 2′-position ofthe sugar moiety is better accommodated in an A-form duplex than aB-form duplex. Thus, a 2′-substituent on the 3′-terminus of adinucleoside monophosphate is thought to exert a number of effects onthe stacking conformation: steric repulsion, furanose puckeringpreference, electrostatic repulsion, hydrophobic attraction, andhydrogen bonding capabilities. These substituent effects are thought tobe determined by the molecular size, electronegativity, andhydrophobicity of the substituent. Melting temperatures of complementarystrands is also increased with the 2′-substituted adenosinediphosphates. It is not clear whether the 3′-endo preference of theconformation or the presence of the substituent is responsible for theincreased binding. However, greater overlap of adjacent bases (stacking)can be achieved with the 3′-endo conformation.

One synthetic 2′-modification that imparts increased nuclease resistanceand a very high binding affinity to nucleotides is the 2-methoxyethoxy(2′-MOE, 2′-OCH₂CH₂OCH₃) side chain (Baker et al., J. Biol. Chem., 1997,272, 11944-12000). One of the immediate advantages of the 2′-MOEsubstitution is the improvement in binding affinity, which is greaterthan many similar 2′ modifications such as O-methyl, O-propyl, andO-aminopropyl. Oligonucleotides having the 2′-O-methoxyethyl substituentalso have been shown to be antisense inhibitors of gene expression withpromising features for in vivo use (Martin, P., Hely. Chim. Acta, 1995,78, 486-504; Altmann et al., Chimia, 1996, 50, 168-176; Altmann et al.,Biochem. Soc. Trans., 1996, 24, 630-637; and Altmann et al., NucleosidesNucleotides, 1997, 16, 917-926). Relative to DNA, the oligonucleotideshaving the 2′-MOE modification displayed improved RNA affinity andhigher nuclease resistance. Chimeric oligonucleotides having 2′-MOEsubstituents in the wing nucleosides and an internal region ofdeoxy-phosphorothioate nucleotides (also termed a gapped oligonucleotideor gapmer) have shown effective reduction in the growth of tumors inanimal models at low doses. 2′-MOE substituted oligonucleotides havealso shown outstanding promise as antisense agents in several diseasestates. One such MOE substituted oligonucleotide is presently beinginvestigated in clinical trials for the treatment of CMV retinitis.

To better understand the higher RNA affinity of 2′-O-methoxyethylsubstituted RNA and to examine the conformational properties of the2′-O-methoxyethyl substituent, two dodecamer oligonucleotides weresynthesized having SEQ ID NO: 54 (CGC GAA UUC GCG) and SEQ ID NO: 55(GCG CUU AAG CGC). These self-complementary strands have every2′-position modified with a 2′-O-methoxyethyl. The duplex wascrystallized at a resolution of 1.7 Ångstrom and the crystal structurewas determined. The conditions used for the crystallization were 2 mMoligonucleotide, 50 mM Na Hepes pH 6.2-7.5, 10.50 mM MgCl₂, 15% PEG 400.The crystal data showed: space group C2, cell constants a=41.2 Å, b=34.4 Å, c=46.6 Å, □=92.4° . The resolution was 1.7 Å at −170° C. Thecurrent R=factor was 20% (R_(free) 26%).

This crystal structure is believed to be the first crystal structure ofa fully modified RNA oligonucleotide analogue. The duplex adopts anoverall A-form conformation and all modified sugars display C3′-endopucker. In most of the 2′-O-substituents, the torsion angle around theA′-B′ bond, as depicted in Structure II below, of the ethylene glycollinker has a gauche conformation. For 2′-O-MOE, A′ and B′ of StructureII below are methylene moieties of the ethyl portion of the MOE and R′is the methoxy portion.

In the crystal, the 2′-0-MOE RNA duplex adopts a general orientationsuch that the crystallographic 2-fold rotation axis does not coincidewith the molecular 2-fold rotation axis. The duplex adopts the expectedA-type geometry and all of the 24 2′-O-MOE substituents were visible inthe electron density maps at full resolution. The electron density mapsas well as the temperature factors of substituent atoms indicateflexibility of the 2′-O-MOE substituent in some cases.

Most of the 2′-O-MOE substituents display a gauche conformation aroundthe C-C bond of the ethyl linker. However, in two cases, a transconformation around the C-C bond is observed. The lattice interactionsin the crystal include packing of duplexes against each other via theirminor grooves. Therefore, for some residues, the conformation of the2′-O-substituent is affected by contacts to an adjacent duplex. Ingeneral, variations in the conformation of the substituents (e.g. g⁺ org⁻ around the C—C bonds) create a range of interactions betweensubstituents, both inter-strand, across the minor groove, andintra-strand. At one location, atoms of substituents from two residuesare in van der Waals contact across the minor groove. Similarly, a closecontact occurs between atoms of substituents from two adjacentintra-strand residues.

Previously determined crystal structures of A-DNA duplexes were forthose that incorporated isolated 2′-O-methyl T residues. In the crystalstructure noted above for the 2′-O-MOE substituents, a conservedhydration pattern has been observed for the 2′-0-MOE residues. A singlewater molecule is seen located between O2′, O3′ and the methoxy oxygenatom of the substituent, forming contacts to all three of between 2.9and 3.4 Å. In addition, oxygen atoms of substituents are involved inseveral other hydrogen bonding contacts. For example, the methoxy oxygenatom of a particular 2′-O-substituent forms a hydrogen bond to N3 of anadenosine from the opposite strand via a bridging water molecule.

In several cases a water molecule is trapped between the oxygen atomsO2′, O3′ and OC′ of modified nucleosides. 2′-O-MOE substituents withtrans conformation around the C-C bond of the ethylene glycol linker areassociated with close contacts between OC′ and N2 of a guanosine fromthe opposite strand, and, water-mediated, between OC' and N3(G). Whencombined with the available thermodynamic data for duplexes containing2′-O-MOE modified strands, this crystal structure allows for furtherdetailed structure-stability analysis of other modifications.

In extending the crystallographic structure studies, molecular modelingexperiments were performed to study further enhanced binding affinity ofoligonucleotides having 2′-O-modifications. The computer simulationswere conducted on compounds of SEQ ID NO: 7, above, having2′-O-modifications located at each of the nucleosides of theoligonucleotide. The simulations were performed with the oligonucleotidein aqueous solution using the AMBER force field method (Cornell et al.,J. Am. Chem. Soc., 1995, 117, 5179-5197)(modeling software package fromUCSF, San Francisco, Calif.). The calculations were performed on anIndigo2 SGI machine (Silicon Graphics, Mountain View, Calif.).

Further 2′-O-modifications that will have a 3′-endo sugar influenceinclude those having a ring structure that incorporates a two atomportion corresponding to the A′ and B′ atoms of Structure II. The ringstructure is attached at the 2′ position of a sugar moiety of one ormore nucleosides that are incorporated into an oligonucleotide. The2′-oxygen of the nucleoside links to a carbon atom corresponding to theA′ atom of Structure II. These ring structures can be aliphatic,unsaturated aliphatic, aromatic or heterocyclic. A further atom of thering (corresponding to the B′ atom of Structure II), bears a furtheroxygen atom, or a sulfur or nitrogen atom. This oxygen, sulfur ornitrogen atom is bonded to one or more hydrogen atoms, alkyl moieties,or haloalkyl moieties, or is part of a further chemical moiety such as aureido, carbamate, amide or amidine moiety. The remainder of the ringstructure restricts rotation about the bond joining these two ringatoms. This assists in positioning the “further oxygen, sulfur ornitrogen atom” (part of the R position as described above) such that thefurther atom can be located in close proximity to the 3′-oxygen atom(O3′) of the nucleoside.

Another preferred 2′-sugar substituent group that gives a 3′-endo sugarconformational geometry is the 2′-OMe group. 2′-Substitution ofguanosine, cytidine, and uridine dinucleoside phosphates with the 2′-OMegroup showed enhanced stacking effects with respect to the correspondingnative (2′-OH) species leading to the conclusion that the sugar isadopting a C3′-endo conformation. In this case, it is believed that thehydrophobic attractive forces of the methyl group tend to overcome thedestabilizing effects of its steric bulk.

The ability of oligonucleotides to bind to their complementary targetstrands is compared by determining the melting temperature (T_(m)) ofthe hybridization complex of the oligonucleotide and its complementarystrand. The melting temperature (T_(m)), a characteristic physicalproperty of double helices, denotes the temperature (in degreescentigrade) at which 50% helical (hybridized) versus coil (unhybridized)forms are present. T_(m) is measured by using the UV spectrum todetermine the formation and breakdown (melting) of the hybridizationcomplex. Base stacking, which occurs during hybridization, isaccompanied by a reduction in UV absorption (hypochromicity).Consequently, a reduction in UV absorption indicates a higher T_(m). Thehigher the T_(m), the greater the strength of the bonds between thestrands.

Freier and Altmann, Nucleic Acids Research, (1997) 25:4429-4443, havepreviously published a study on the influence of structuralmodifications of oligonucleotides on the stability of their duplexeswith target RNA. In this study, the authors reviewed a series ofoligonucleotides containing more than 200 different modifications thathad been synthesized and assessed for their hybridization affinity andTm. Sugar modifications studied included substitutions on the2′-position of the sugar, 3′-substitution, replacement of the 4′-oxygen,the use of bicyclic sugars, and four member ring replacements. Severalnucleobase modifications were also studied including substitutions atthe 5, or 6 position of thymine, modifications of pyrimidine heterocycleand modifications of the purine heterocycle. Modified internucleosidelinkages were also studied including neutral, phosphorus andnon-phosphorus containing internucleoside linkages.

Increasing the percentage of C3′-endo sugars in a modifiedoligonucleotide targeted to an RNA target strand should preorganize thisstrand for binding to RNA. Of the several sugar modifications that havebeen reported and studied in the literature, the incorporation ofelectronegative substituents such as 2′-fluoro or 2′-alkoxy shift thesugar conformation towards the 3′ endo (northern) pucker conformation.This preorganizes an oligonucleotide that incorporates suchmodifications to have an A-form conformational geometry. This A-formconformation results in increased binding affinity of theoligonucleotide to a target RNA strand.

Molecular modeling experiments were performed to study further enhancedbinding affinity of oligonucleotides having 2′-O-modifications. Computersimulations were conducted on compounds having SEQ ID NO: 54, r(CGC GAAUUC GCG), having 2′-O-modifications of the invention located at each ofthe nucleoside of the oligonucleotide. The simulations were performedwith the oligonucleotide in aqueous solution using the AMBER force fieldmethod (Cornell et al., J. Am. Chem. Soc., 1995, 117,5179-5197)(modeling software package from UCSF, San Francisco, Calif.).The calculations were performed on an Indigo2 SGI machine (SiliconGraphics, Mountain View, Calif.).

In addition, for 2′-substituents containing an ethylene glycol motif, agauche interaction between the oxygen atoms around the O—C—C—O torsionof the side chain may have a stabilizing effect on the duplex (Freieribid.). Such gauche interactions have been observed experimentally for anumber of years (Wolfe et al., Acc. Chem. Res., 1972, 5, 102; Abe etal., J. Am. Chem. Soc., 1976, 98, 468). This gauche effect may result ina configuration of the side chain that is favorable for duplexformation. The exact nature of this stabilizing configuration has notyet been explained. While we do not want to be bound by theory, it maybe that holding the O—C—C—O torsion in a single gauche configuration,rather than a more random distribution seen in an alkyl side chain,provides an entropic advantage for duplex formation.

Representative 2′-substituent groups amenable to the present inventionthat give A-form conformational properties (3′-endo) to the resultantduplexes include 2′-O-alkyl, 2′-O-substituted alkyl and 2′-fluorosubstituent groups. Preferred for the substituent groups are variousalkyl and aryl ethers and thioethers, amines and monoalkyl and dialkylsubstituted amines. It is further intended that multiple modificationscan be made to one or more of the compositions of the invention atmultiple sites of one or more monomeric subunits (nucleosides arepreferred) and or internucleoside linkages to enhance properties such asbut not limited to activity in a selected application. Tables I throughVII list nucleoside and internucleotide linkagemodifications/replacements that have been shown to give a positive ∈ Tmper modification when the modification/replacement was made to a DNAstrand that was hybridized to an RNA complement.

TABLE I Modified DNA strand having 2′-substituent groups that gave anoverall increase in Tm against an RNA complement: Positive ∈Tm/mod2′-substituents 2′-OH 2′-O—C₁-C₄ alkyl 2′-O—(CH₂)₂CH₃ 2′-O—CH₂CH═CH₂2′-F 2′-O—(CH₂)₂—O—CH₃ 2′-[O—(CH₂)₂]₂—O—CH₃ 2′-[O—(CH₂)₂]₃—O—CH₃2′-[O—(CH₂)₂]₄—O—CH₃ 2′-[O—(CH₂)₂]₃—O—(CH₂)₈CH₃ 2′-O—(CH₂)₂CF₃2′-O—(CH₂)₂OH 2′-O—(CH₂)₂F 2′-O—CH₂CH(CH₃)F 2′-O—CH₂CH(CH₂OH)OH2′-O—CH₂CH(CH₂OCH₃)OCH₃ 2′-O—CH₂CH(CH₃)OCH₃ 2′-O—CH₂-C₁₄H₇O₂(—C₁₄H₇O₂ =Anthraquinone) 2′-O—(CH₂)₃—NH₂* 2′-O—(CH₂)₄—NH₂* *These modificationscan increase the Tm of oligonucleotides but can also decrease the Tmdepending on positioning and number (motiff dependant).

TABLE II Modified DNA strand having modified sugar ring (see structurex) that gave an overall increase in Tm against an RNA complement:

Positive ∈ Tm/mod Q —S— —CH₂— Note: In general ring oxygen substitutionwith sulfur or methylene had only a minor effect on Tm for the specificmotiffs studied. Substitution at the 2′-position with groups shown tostabilize the duplex were destabilizing when CH₂ replaced the ring O.This is thought to be due to the necessary gauche interaction betweenthe ring O with particular 2′-substituents (for example —O—CH₃ and—(O—CH₂CH₂)₃—O—CH₃.

TABLE III Modified DNA strand having modified sugar ring that give anoverall increase in Tm against an RNA complement:

  Positive ∈ Tm/mod —C(H)R₁ effects OH (R₂, R₃ both = H) CH₃* CH₂OH*OCH₃* *These modifications can increase the Tm of oligonucleotides butcan also decrease the Tm depending on positioning and number (motiffdependant).

TABLE IV Modified DNA strand having bicyclic substitute sugarmodifications that give an overall increase in Tm against an RNAcomplement: Formula Positive ∈ Tm/mod I + II +

TABLE V Modified DNA strand having modified heterocyclic base moietiesthat give an overall increase in Tm against an RNA complement:Modification/Formula Positive ∈ Tm/mod Heterocyclic base 2-thioTmodifications 2′-O-methylpseudoU 7-halo-7-deaza purines7-propyne-7-deaza purines 2-aminoA(2,6-diaminopurine)Modification/Formula Positive ∈ Tm/mod

(R₂, R₃ = H), R₁ = Br C/C—CH₃ (CH₂)₃NH₂ CH₃ Motiffs-disubstitution R₁ =C/C—CH₃, R₂ = H, R₃ = F R₁ = C/C—CH₃, R₂ = H R₃ = O—(CH₂)₂—O—CH₃ R₁ =O—CH₃, R₂ = H, R₃ = O—(CH₂)₂—O—CH₃* *This modification can increase theTm of oligonucleotides but can also decrease the Tm depending onpositioning and number (motiff dependant).

Substitution at R₁ can be stabilizing, substitution at R₂ is generallygreatly destabilizing (unable to form anti conformation), motiffs withstabilizing 5 and 2′-substituent groups are generally additive e.g.increase stability.

Substitution of the O4 and O2 positions of 2′-O-methyl uridine wasgreatly duplex destabilizing as these modifications remove hydrogenbinding sites that would be an expected result. 6-Aza T also showedextreme destabilization as this substitution reduces the pK_(a) andshifts the nucleoside toward the enol tautomer resulting in reducedhydrogen bonding.

TABLE VI DNA strand having at least one modified phosphorus containinginternucleoside linkage and the effect on the Tm against an RNAcomplement: ∈Tm/mod+ ∈Tm/mod− phosphoramidate (the 3′-bridgingphosphorothioate¹ atom replaced with an N(H)R phosphoramidate¹ group,stabilization effect methyl phosphonates¹ enhanced when also have 2′-F)(¹ one of the non-bridging oxygen atoms replaced with S, N(H)R or —CH₃)

TABLE VII DNA strand having at least one non-phosphorus containinginternucleoside linkage and the effect on the Tm against an RNAcomplement: Positive ∈Tm/mod —CH₂C(═O)NHCH₂—* —CH₂C(═O)N(CH₃)CH₂—*—CH₂C(═O)N(CH₂CH₂CH₃)CH₂—* —CH₂C(═O)N(H)CH₂—(motiff with 5′-propyne onT's) —CH₂N(H)C(═O)CH₂—* —CH₂N(CH₃)OCH₂—* —CH₂N(CH₃)N(CH₃)CH₂—* *Thismodification can increase the Tm of oligonucleotides but can alsodecrease the Tm depending on positioning and number (motiff dependant).Notes: In general carbon chain internucleotide linkages weredestabilizing to duplex formation. This destabilization was not assevere when double and tripple bonds were utilized. The use of glycoland flexible ether linkages were also destabilizing.

Preferred ring structures of the invention for inclusion as a 2′-Omodification include cyclohexyl, cyclopentyl and phenyl rings as well asheterocyclic rings having spacial footprints similar to cyclohexyl,cyclopentyl and phenyl rings. Particularly preferred 2′-O-substituentgroups of the invention are listed below including an abbreviation foreach:

-   -   2′-O-(trans 2-methoxy cyclohexyl)—2′-O-(TMCHL)    -   2′-O-(trans 2-methoxy cyclopentyl)—2′-O-(TMCPL)    -   2′-O-(trans 2-ureido cyclohexyl)—2′-O-(TUCHL)    -   2′-O-(trans 2-methoxyphenyl)—2′-O-(2MP)

Structural details for duplexes incorporating such 2-O-substituents wereanalyzed using the described AMBER force field program on the Indigo2SGI machine. The simulated structure maintained a stable A-form geometrythroughout the duration of the simulation. The presence of the 2′substitutions locked the sugars in the C3′-endo conformation.

The simulation for the TMCHL modification revealed that the 2′-O-(TMCHL)side chains have a direct interaction with water molecules solvating theduplex. The oxygen atoms in the 2′-O-(TMCHL) side chain are capable offorming a water-mediated interaction with the 3′ oxygen of the phosphatebackbone. The presence of the two oxygen atoms in the 2′-O-(TMCHL) sidechain gives rise to favorable gauche interactions. The barrier forrotation around the O—C—C—O torsion is made even larger by this novelmodification. The preferential preorganization in an A-type geometryincreases the binding affinity of the 2′-O-(TMCHL) to the target RNA.The locked side chain conformation in the 2′-O-(TMCHL) group created amore favorable pocket for binding water molecules. The presence of thesewater molecules played a key role in holding the side chains in thepreferable gauche conformation. While not wishing to be bound by theory,the bulk of the substituent, the diequatorial orientation of thesubstituents in the cyclohexane ring, the water of hydration and thepotential for trapping of metal ions in the conformation generated willadditionally contribute to improved binding affinity and nucleaseresistance of oligonucleotides incorporating nucleosides having this2′-O-modification.

As described for the TMCHL modification above, identical computersimulations of the 2′-O-(TMCPL), the 2′-O-(2MP) and 2′-O-(TUCHL)modified oligonucleotides in aqueous solution also illustrate thatstable A-form geometry will be maintained throughout the duration of thesimulation. The presence of the 2′ substitution will lock the sugars inthe C3′-endo conformation and the side chains will have directinteraction with water molecules solvating the duplex. The oxygen atomsin the respective side chains are capable of forming a water-mediatedinteraction with the 3′ oxygen of the phosphate backbone. The presenceof the two oxygen atoms in the respective side chains give rise to thefavorable gauche interactions. The barrier for rotation around therespective O—C—C—O torsions will be made even larger by respectivemodification. The preferential preorganization in A-type geometry willincrease the binding affinity of the respective 2′-O-modifiedoligonucleotides to the target RNA. The locked side chain conformationin the respective modifications will create a more favorable pocket forbinding water molecules. The presence of these water molecules plays akey role in holding the side chains in the preferable gaucheconformation. The bulk of the substituent, the diequatorial orientationof the substituents in their respective rings, the water of hydrationand the potential trapping of metal ions in the conformation generatedwill all contribute to improved binding affinity and nuclease resistanceof oligonucleotides incorporating nucleosides having these respective2′-O-modification.

Ribose conformations in C2′-modified nucleosides containing S-methylgroups were examined. To understand the influence of 2′-O-methyl and2′-S-methyl groups on the conformation of nucleosides, we evaluated therelative energies of the 2′-O- and 2′-S-methylguanosine, along withnormal deoxyguanosine and riboguanosine, starting from both C2′-endo andC3′-endo conformations using ab initio quantum mechanical calculations.All the structures were fully optimized at HF/6-31G* level and singlepoint energies with electron-correlation were obtained at theMP2/6-31G*//HF/6-31G* level. As shown in Table 1, the C2′-endoconformation of deoxyguanosine is estimated to be 0.6 kcal/mol morestable than the C3′-endo conformation in the gas-phase. Theconformational preference of the C2′-endo over the C3′-endo conformationappears to be less dependent upon electron correlation as revealed bythe MP2/6-31G*//HF/6-31G* values which also predict the same differencein energy. The opposite trend is noted for riboguanosine. At theHF/6-31G* and MP2/6-31G*//HF/6-31G* levels, the C3′-endo form ofriboguanosine is shown to be about 0.65 and 1.41 kcal/mol more stablethan the C2′ endo form, respectively.

TABLE 1 Relative energies* of the C3′-endo and C2′-endo conformations ofrepresentative nucleosides. CONTINUUM HF/6-31G MP2/6-31-G MODEL AMBER dG0.60 0.56 0.88 0.65 rG −0.65 −1.41 −0.28 −2.09 2′-O-MeG −0.89 −1.79−0.36 −0.86 2′-S-MeG 2.55 1.41 3.16 2.43 *energies are in kcal/molrelative to the C2′-endo conformation

Table 1 also includes the relative energies of 2′-O-methylguanosine and2′-S-methylguanosine in C2′-endo and C3′-endo conformation. This dataindicates the electronic nature of C2′-substitution has a significantimpact on the relative stability of these conformations. Substitution ofthe 2′-O-methyl group increases the preference for the C3′-endoconformation (when compared to riboguanosine) by about 0.4 kcal/mol atboth the HF/6-31G* and MP2/6-31G*//HF/6-31G* levels. In contrast, the2′-S-methyl group reverses the trend. The C2′-endo conformation isfavored by about 2.6 kcal/mol at the HF/6-31G* level, while the samedifference is reduced to 1.41 kcal/mol at the MP2/6-31G*//HF/6-31G*level. For comparison, and also to evaluate the accuracy of themolecular mechanical force-field parameters used for the 2′-O-methyl and2′-S-methyl substituted nucleosides, we have calculated the gas phaseenergies of the nucleosides. The results reported in Table 1 indicatethat the calculated relative energies of these nucleosides comparequalitatively well with the ab initio calculations.

Additional calculations were also performed to gauge the effect ofsolvation on the relative stability of nucleoside conformations. Theestimated solvation effect using HF/6-31G* geometries confirms that therelative energetic preference of the four nucleosides in the gas-phaseis maintained in the aqueous phase as well (Table 1). Solvation effectswere also examined using molecular dynamics simulations of thenucleosides in explicit water. From these trajectories, one can observethe predominance of C2′-endo conformation for deoxyriboguanosine and2′-S-methylriboguanosine while riboguanosine and2′-O-methylriboguanosine prefer the C3′-endo conformation. These resultsare in much accord with the available NMR results on2′-S-methylribonucleosides. NMR studies of sugar puckering equilibriumusing vicinal spin-coupling constants have indicated that theconformation of the sugar ring in 2′-S-methylpyrimidine nucleosides showan average of >75% S-character, whereas the corresponding purine analogsexhibit an average of >90% S-pucker [Fraser, A., Wheeler, P., Cook, P.D. and Sanghvi, Y. S., J. Heterocycl. Chem., 1993, 30, 1277-1287]. Itwas observed that the 2′-S-methyl substitution in deoxynucleosideconfers more conformational rigidity to the sugar conformation whencompared with deoxyribonucleosides.

Structural features of DNA:RNA, OMe-DNA:RNA and SMe-DNA:RNA hybrids werealso observed. The average RMS deviation of the DNA:RNA structure fromthe starting hybrid coordinates indicate the structure is stabilizedover the length of the simulation with an approximate average RMSdeviation of 1.0 Å. This deviation is due, in part, to inherentdifferences in averaged structures (i.e. the starting conformation) andstructures at thermal equilibrium. The changes in sugar puckerconformation for three of the central base pairs of this hybrid are ingood agreement with the observations made in previous NMR studies. Thesugars in the RNA strand maintain very stable geometries in the C3′-endoconformation with ring pucker values near 0° . In contrast, the sugarsof the DNA strand show significant variability.

The average RMS deviation of the OMe-DNA:RNA is approximately 1.2 Å fromthe starting A-form conformation; while the SMe-DNA:RNA shows a slightlyhigher deviation (approximately 1.8 Å) from the starting hybridconformation. The SMe-DNA strand also shows a greater variance in RMSdeviation, suggesting the S-methyl group may induce some structuralfluctuations. The sugar puckers of the RNA complements maintain C3′-endopuckering throughout the simulation. As expected from the nucleosidecalculations, however, significant differences are noted in thepuckering of the OMe-DNA and SMe-DNA strands, with the former adoptingC3′-endo, and the latter, C1′-exo/C2′-endo conformations.

An analysis of the helicoidal parameters for all three hybrid structureshas also been performed to further characterize the duplex conformation.Three of the more important axis-basepair parameters that distinguishthe different forms of the duplexes, X-displacement, propeller twist,and inclination, are reported in Table 2. Usually, an X-displacementnear zero represents a B-form duplex; while a negative displacement,which is a direct measure of deviation of the helix from the helicalaxis, makes the structure appear more A-like in conformation. In A-formduplexes, these values typically vary from −4Å to −5Å. In comparingthese values for all three hybrids, the SMe_DNA:RNA hybrid shows themost deviation from the A-form value, the OMe_DNA:RNA shows the least,and the DNA:RNA is intermediate. A similar trend is also evident whencomparing the inclination and propeller twist values with ideal A-formparameters. These results are further supported by an analysis of thebackbone and glycosidic torsion angles of the hybrid structures.Glycosidic angles (X) of A-form geometries, for example, are typicallynear −159° while B form values are near −102° . These angles are foundto be −162°, −133° , and −108° for the OMe-DNA, DNA, and SMe-DNAstrands, respectively. All RNA complements adopt an X angle close to−160° . In addition, “crankshaft” transitions were also noted in thebackbone torsions of the central UpU steps of the RNA strand in theSMe-DNA:RNA and DNA;RNA hybrids. Such transitions suggest some localconformational changes may occur to relieve a less favorable globalconformation. Taken overall, the results indicate the amount ofA-character decreases as OMe-DNA:RNA>DNA:RNA>SMe-DNA:RNA, with thelatter two adopting more intermediate conformations when compared to A-and B-form geometries.

TABLE 2 Average helical parameters derived from the last 500 ps ofsimulation time. (canonical A-and B-form values are given forcomparison) Helicoidal B-DNA B-DNA A-DNA Parameter (x-ray) (fibre)(fibre) DNA:RNA OMe_DNA:RNA SMe_DNA:RNA X-disp 1.2 0.0 −5.3 −4.5 −5.4−3.5 Inclination −2.3 1.5 20.7 11.6 15.1 0.7 Propeller −16.4 −13.3 −7.5−12.7 −15.8 −10.3

Stability of C2′-modified DNA:RNA hybrids was determined. Although theoverall stability of the DNA:RNA hybrids depends on several factorsincluding sequence-dependencies and the purine content in the DNA or RNAstrands DNA:RNA hybrids are usually less stable than RNA:RNA duplexesand, in some cases, even less stable than DNA:DNA duplexes. Availableexperimental data attributes the relatively lowered stability of DNA:RNAhybrids largely to its intermediate conformational nature betweenDNA:DNA (B-family) and RNA:RNA (A-family) duplexes. The overallthermodynamic stability of nucleic acid duplexes may originate fromseveral factors including the conformation of backbone, base-pairing andstacking interactions. While it is difficult to ascertain the individualthermodynamic contributions to the overall stabilization of the duplex,it is reasonable to argue that the major factors that promote increasedstability of hybrid duplexes are better stacking interactions(electrostatic π-π interactions) and more favorable groove dimensionsfor hydration. The C2′-S-methyl substitution has been shown todestabilize the hybrid duplex. The notable differences in the risevalues among the three hybrids may offer some explanation. While the2′-S-methyl group has a strong influence on decreasing the base-stackingthrough high rise values (˜3.2 Å), the 2′-O-methyl group makes theoverall structure more compact with a rise value that is equal to thatof A-form duplexes (˜2.6 Å). Despite its overall A-like structuralfeatures, the SMe_DNA:RNA hybrid structure possesses an average risevalue of 3.2 Å which is quite close to that of B-family duplexes. Infact, some local base-steps (CG steps) may be observed to have unusuallyhigh rise values (as high as 4.5Å). Thus, the greater destabilization of2′-S-methyl substituted DNA:RNA hybrids may be partly attributed to poorstacking interactions.

It has been postulated that RNase H binds to the minor groove of RNA:DNAhybrid complexes, requiring an intermediate minor groove width betweenideal A- and B-form geometries to optimize interactions between thesugar phosphate backbone atoms and RNase H. A close inspection of theaveraged structures for the hybrid duplexes using computer simulationsreveals significant variation in the minor groove width dimensions asshown in Table 3. Whereas the O-methyl substitution leads to a slightexpansion of the minor groove width when compared to the standardDNA:RNA complex, the S-methyl substitution leads to a generalcontraction (approximately 0.9 Å). These changes are most likely due tothe preferred sugar puckering noted for the antisense strands whichinduce either A- or B-like single strand conformations. In addition tominor groove variations, the results also point to potential differencesin the steric makeup of the minor groove. The O-methyl group points intothe minor groove while the S-methyl is directed away towards the majorgroove. Essentially, the S-methyl group has flipped through the basesinto the major groove as a consequence of C2′-endo puckering.

TABLE 3 Minor groove widths averaged over the last 500 ps of simulationtime Phosphate DNA:RNA RNA:RNA Distance DNA:RNA OMe_DNA:RNA SMe_DNA:RNA(B-form) (A-form) P5-P20 15.27 16.82 13.73 14.19 17.32 P6-P19 15.5216.79 15.73 12.66 17.12 P7-P18 15.19 16.40 14.08 11.10 16.60 P8-P1715.07 16.12 14.00 10.98 16.14 P9-P16 15.29 16.25 14.98 11.65 16.93P10-P15 15.37 16.57 13.92 14.05 17.69Chemistries Defined

Unless otherwise defined herein, alkyl means C₁-C₁₂, preferably C₁-C₈,and more preferably C₁-C₆, straight or (where possible) branched chainaliphatic hydrocarbyl.

Unless otherwise defined herein, heteroalkyl means C₁-C₁₂, preferablyC₁-C₈, and more preferably C₁-C₆, straight or (where possible) branchedchain aliphatic hydrocarbyl containing at least one, and preferablyabout 1 to about 3, hetero atoms in the chain, including the terminalportion of the chain. Preferred heteroatoms include N, O and S.

Unless otherwise defined herein, cycloalkyl means C₃-C₁₂, preferablyC₃-C₈, and more preferably C₃-C₆, aliphatic hydrocarbyl ring.

Unless otherwise defined herein, alkenyl means C₂-C₁₂, preferably C₂-C₈,and more preferably C₂-C₆ alkenyl, which may be straight or (wherepossible) branched hydrocarbyl moiety, which contains at least onecarbon-carbon double bond.

Unless otherwise defined herein, alkynyl means C₂-C₁₂, preferably C₂-C₈,and more preferably C₂-C₆ alkynyl, which may be straight or (wherepossible) branched hydrocarbyl moiety, which contains at least onecarbon-carbon triple bond.

Unless otherwise defined herein, heterocycloalkyl means a ring moietycontaining at least three ring members, at least one of which is carbon,and of which 1, 2 or three ring members are other than carbon.Preferably the number of carbon atoms varies from 1 to about 12,preferably 1 to about 6, and the total number of ring members variesfrom three to about 15, preferably from about 3 to about 8. Preferredring heteroatoms are N, O and S. Preferred heterocycloalkyl groupsinclude morpholino, thiomorpholino, piperidinyl, piperazinyl,homopiperidinyl, homopiperazinyl, homomorpholino, homothiomorpholino,pyrrolodinyl, tetrahydrooxazolyl, tetrahydroimidazolyl,tetrahydrothiazolyl, tetrahydroisoxazolyl, tetrahydropyrrazolyl,furanyl, pyranyl, and tetrahydroisothiazolyl.

Unless otherwise defined herein, aryl means any hydrocarbon ringstructure containing at least one aryl ring. Preferred aryl rings haveabout 6 to about 20 ring carbons. Especially preferred aryl ringsinclude phenyl, napthyl, anthracenyl, and phenanthrenyl.

Unless otherwise defined herein, hetaryl means a ring moiety containingat least one fully unsaturated ring, the ring consisting of carbon andnon-carbon atoms. Preferably the ring system contains about 1 to about 4rings. Preferably the number of carbon atoms varies from 1 to about 12,preferably 1 to about 6, and the total number of ring members variesfrom three to about 15, preferably from about 3 to about 8. Preferredring heteroatoms are N, O and S. Preferred hetaryl moieties includepyrazolyl, thiophenyl, pyridyl, imidazolyl, tetrazolyl, pyridyl,pyrimidinyl, purinyl, quinazolinyl, quinoxalinyl, benzimidazolyl,benzothiophenyl, etc.

Unless otherwise defined herein, where a moiety is defined as a compoundmoiety, such as hetarylalkyl (hetaryl and alkyl), aralkyl (aryl andalkyl), etc., each of the sub-moieties is as defined herein.

Unless otherwise defined herein, an electron withdrawing group is agroup, such as the cyano or isocyanato group that draws electroniccharge away from the carbon to which it is attached. Other electronwithdrawing groups of note include those whose electronegativitiesexceed that of carbon, for example halogen, nitro, or phenyl substitutedin the ortho- or para-position with one or more cyano, isothiocyanato,nitro or halo groups.

Unless otherwise defined herein, the terms halogen and halo have theirordinary meanings. Preferred halo (halogen) substituents are Cl, Br, andI.

The aforementioned optional substituents are, unless otherwise hereindefined, suitable substituents depending upon desired properties.Included are halogens (Cl, Br, I), alkyl, alkenyl, and alkynyl moieties,NO2, NH3 (substituted and unsubstituted), acid moieties (e.g. —CO₂H,—OSO₃H₂, etc.), heterocycloalkyl moieties, hetaryl moieties, arylmoieties, etc.

In all the preceding formulae, the squiggle (˜) indicates a bond to anoxygen or sulfur of the 5′-phosphate. Phosphate protecting groupsinclude those described in U.S. Pat. Nos. 5,760,209, 5,614,621,6,051,699, 6,020,475, 6,326,478, 6,169,177, 6,121,437, 6,465,628 each ofwhich is expressly incorporated herein by reference in its entirety.

Oligomer Synthesis

Oligomerization of modified and unmodified nucleosides is performedaccording to literature procedures for DNA (Protocols forOligonucleotides and Analogs, Ed. Agrawal (1993), Humana Press) and/orRNA (Scaringe, Methods (2001), 23, 206-217. Gait et al., Applications ofChemically synthesized RNA in RNA:Protein Interactions, Ed. Smith(1998), 1-36. Gallo et al., Tetrahedron (2001), 57, 5707-5713) synthesisas appropriate. In addition specific protocols for the synthesis ofcompositions of the invention are illustrated in the examples below.

The oligonucleotides used in accordance with this invention may beconveniently and routinely made through the well-known technique ofsolid phase synthesis. Equipment for such synthesis is sold by severalvendors including, for example, Applied Biosystems (Foster City,Calif.). Any other means for such synthesis known in the art mayadditionally or alternatively be employed. It is well known to usesimilar techniques to prepare oligonucleotides such as thephosphorothioates and alkylated derivatives.

The present invention is also useful for the preparation ofoligonucleotides incorporating at least one 2′-O-protected nucleoside.After incorporation and appropriate deprotection the 2′-O-protectednucleoside will be converted to a ribonucleoside at the position ofincorporation. The number and position of the 2-ribonucleoside units inthe final oligonucleotide can vary from one at any site or the strategycan be used to prepare up to a full 2′-OH modified oligonucleotide. All2′-O-protecting groups amenable to the synthesis of oligonucleotides areincluded in the present invention. In general a protected nucleoside isattached to a solid support by for example a succinate linker. Then theoligonucleotide is elongated by repeated cycles of deprotecting the5′-terminal hydroxyl group, coupling of a further nucleoside unit,capping and oxidation (alternatively sulfurization). In a morefrequently used method of synthesis the completed oligonucleotide iscleaved from the solid support with the removal of phosphate protectinggroups and exocyclic amino protecting groups by treatment with anammonia solution. Then a further deprotection step is normally requiredfor removal of the more specialized protecting groups used for theprotection of 2′-hydroxyl groups thereby affording the fully deprotectedoligonucleotide.

A large number of 2′-O-protecting groups have been used for thesynthesis of oligoribonucleotides but over the years more effectivegroups have been discovered. The key to an effective 2′-O-protectinggroup is that it is capable of selectively being introduced at the2′-O-position and that it can be removed easily after synthesis withoutthe formation of unwanted side products. The protecting group also needsto be inert to the normal deprotecting, coupling, and capping stepsrequired for oligoribonucleotide synthesis. Some of the protectinggroups used initially for oligoribonucleotide synthesis includedtetrahydropyran-1-yl and 4-methoxytetrahydropyran-4-yl. These two groupsare not compatible with all 5′-O-protecting groups so modified versionswere used with 5′-DMT groups such as1-(2-fluorophenyl)-4-methoxypiperidin-4-yl (Fpmp). Reese has identifieda number of piperidine derivatives (like Fpmp) that are useful in thesynthesis of oligoribonucleotides including1-[(chloro-4-methyl)phenyl]-4′-methoxypiperidin-4-yl (Reese et al.,Tetrahedron Lett., 1986, (27), 2291). Another approach was to replacethe standard 5′-DMT (dimethoxytrityl) group with protecting groups thatwere removed under non-acidic conditions such as levulinyl and9-fluorenylmethoxycarbonyl. Such groups enable the use of acid labile2′-protecting groups for oligoribonucleotide synthesis. Another morewidely used protecting group initially used for the synthesis ofoligoribonucleotides was the t-butyldimethylsilyl group (Ogilvie et al.,Tetrahedron Lett., 1974, 2861; Hakimelahi et al., Tetrahedron Lett.,1981, (22), 2543; and Jones et al., J. Chem. Soc. Perkin I., 2762). The2′-O-protecting groups can require special reagents for their removalsuch as for example the t-butyldimethylsily group is normally removedafter all other cleaving/deprotecting steps by treatment of theoligonucleotide with tetrabutylammonium fluoride (TBAF).

One group of researchers examined a number of 2′-O-protecting groups(Pitsch, S., Chimia, 2001, (55), 320-324.) The group examined fluoridelabile and photolabile protecting groups that are removed using moderateconditions. One photolabile group that was examined was the[2-(nitrobenzyl)oxy]methyl (nbm) protecting group (Schwartz et al.,Bioorg. Med. Chem. Lett., 1992, (2), 1019.) Other groups examinedincluded a number structurally related formaldehyde acetal-derived,2′-O-protecting groups. Also prepared were a number of relatedprotecting groups for preparing 2′-O-alkylated nucleosidephosphoramidites including 2′-O-[(triisopropylsilyl)oxy]methyl(2′-O—CH₂—O—Si(iPr)₃, TOM). One 2′-O-protecting group that was preparedto be used orthogonally to the TOM group was2′-O-[(R)-1-(2-nitrophenyl)ethyloxy)methyl] ((R)-mnbm).

Another strategy using a fluoride labile 5′-O-protecting group (non-acidlabile) and an acid labile 2′-O-protecting group has been reported(Scaringe, Stephen A., Methods, 2001, (23) 206-217). A number ofpossible silyl ethers were examined for 5′-O-protection and a number ofacetals and orthoesters were examined for 2′-O-protection. Theprotection scheme that gave the best results was 5′-O-silyl ether-2′-ACE(5′-O-bis(trimethylsiloxy)cyclododecyloxysilyl ether(DOD)-2′-O-bis(2-acetoxyethoxy)methyl (ACE). This approach uses amodified phosphoramidite synthesis approach in that some differentreagents are required that are not routinely used for RNA/DNA synthesis.

Although a lot of research has focused on the synthesis ofoligoribonucleotides the main RNA synthesis strategies that arepresently being used commercially include5′-O-DMT-2′-O-t-butyldimethylsilyl (TBDMS),5′-O-DMT-2′-O-[(1(2-fluorophenyl)-4-methoxypiperidin-4-yl] (FPMP),2′-O-[(triisopropylsilyl)oxy]methyl (2′-O-CH2-O-Si(iPr)3 (TOM), and the5′-O-silyl ether-2′-ACE (5′-O-bis(trimethylsiloxy)cyclododecyloxysilylether (DOD)-2′-O-bis(2-acetoxyethoxy)methyl (ACE). A current list ofsome of the major companies currently offering RNA products includePierce Nucleic Acid Technologies, Dharmacon Research Inc., AmeriBiotechnologies Inc., and Integrated DNA Technologies, Inc. One company,Princeton Separations, is marketing an RNA synthesis activatoradvertised to reduce coupling times especially with TOM and TBDMSchemistries. Such an activator would also be amenable to the presentinvention.

The primary groups being used for commercial RNA synthesis are:

-   -   TBDMS =5′-O-DMT-2′-O-t-butyldimethylsilyl;    -   TOM =2′-O-[(triisopropylsilyl)oxy]methyl;    -   DOD/ACE =(5′-O-bis(trimethylsiloxy)cyclododecyloxysilyl        ether-2′-O-bis(2-acetoxyethoxy)methyl    -   FPMP =5′-O-DMT-2′-O-[1(2-fluorophenyl)-4-methoxypiperidin-4-yl].

All of the aforementioned RNA synthesis strategies are amenable to thepresent invention. Strategies that would be a hybrid of the above e.g.using a 5′-protecting group from one strategy with a 2′-O-protectingfrom another strategy is also amenable to the present invention.

The preparation of ribonucleotides and oligonucleotides having at leastone ribonucleoside incorporated and all the possible configurationsfalling in between these two extremes are encompassed by the presentinvention. The corresponding oligomeric comounds can be hybridized tofurther oligonucleotides including oligoribonucleotides having regionsof complementarity to form double-stranded (duplexed) oligonucleotides.Such double stranded oligonucleotide moieties have been shown in the artto modulate target expression and regulate translation as well as RNAprocesssing via an antisense mechanism. Moreover, the double-strandedmoieties may be subject to chemical modifications (Fire et al., Nature,1998, 391, 806-811; Timmons and Fire, Nature 1998, 395, 854; Timmons etal., Gene, 2001, 263, 103-112; Tabara et al., Science, 1998, 282,430-431; Montgomery et al., Proc. Natl. Acad. Sci. USA, 1998, 95,15502-15507; Tuschl et al., Genes Dev., 1999, 13, 3191-3197; Elbashir etal., Nature, 2001, 411, 494-498; Elbashir et al., Genes Dev. 2001, 15,188-200). For example, such double-stranded moieties have been shown toinhibit the target by the classical hybridization of antisense strand ofthe duplex to the target, thereby triggering enzymatic degradation ofthe target (Tijsterman et al., Science, 2002, 295, 694-697).

The methods of preparing oligonucleotides of the present invention canalso be applied in the areas of drug discovery and target validation.The present invention comprehends the use of the oligonucleotides andpreferred targets identified herein in drug discovery efforts toelucidate relationships that exist between proteins and a disease state,phenotype, or condition. These methods include detecting or modulating atarget peptide comprising contacting a sample, tissue, cell, or organismwith the oligonucleotides of the present invention, measuring thenucleic acid or protein level of the target and/or a related phenotypicor chemical endpoint at some time after treatment, and optionallycomparing the measured value to a non-treated sample or sample treatedwith a further oligonucleotide of the invention. These methods can alsobe performed in parallel or in combination with other experiments todetermine the function of unknown genes for the process of targetvalidation or to determine the validity of a particular gene product asa target for treatment or prevention of a particular disease, condition,or phenotype.

Effect of nucleoside modifications on RNAi activity is evaluatedaccording to existing literature (Elbashir et al., Nature (2001), 411,494-498; Nishikura et al., Cell (2001), 107, 415-416; and Bass et al.,Cell (2000), 101, 235-238.)

Targets of the Invention

“Targeting” a composition of the present invention to a particularnucleic acid molecule, in the context of this invention, can be amultistep process. The process usually begins with the identification ofa target nucleic acid whose function is to be modulated. This targetnucleic acid may be, for example, a cellular gene (or mRNA transcribedfrom the gene) whose expression is associated with a particular disorderor disease state, or a nucleic acid molecule from an infectious agent.

The targeting process usually also includes determination of at leastone target region, segment, or site within the target nucleic acid forthe antisense interaction to occur such that the desired effect, e.g.,modulation of expression, will result. Within the context of the presentinvention, the term “region” as applied to targets is defined as aportion of the target nucleic acid having at least one identifiablestructure, function, or characteristic. Within regions of target nucleicacids are segments. “Segments” are defined as smaller or sub-portions ofregions within a target nucleic acid. “Sites,” as used in the presentinvention, are defined as positions within a target nucleic acid. Theterms region, segment, and site can also be used to describe anoligomeric compound such as an oligonucleotide of the invention such asfor example a gapped oligonucleotide having 3 separate segments.

Since, as is known in the art, the translation initiation codon istypically 5′-AUG (in transcribed mRNA molecules; 5′-ATG in thecorresponding DNA molecule), the translation initiation codon is alsoreferred to as the “AUG codon,” the “start codon” or the “AUG startcodon”. A minority of genes have a translation initiation codon havingthe RNA sequence 5′-GUG, 5′-UUG or 5′-CUG, and 5′-AUA, 5′-ACG and 5′-CUGhave been shown to function in vivo. Thus, the terms “translationinitiation codon” and “start codon” can encompass many codon sequences,even though the initiator amino acid in each instance is typicallymethionine (in eukaryotes) or formylmethionine (in prokaryotes). It isalso known in the art that eukaryotic and prokaryotic genes may have twoor more alternative start codons, any one of which may be preferentiallyutilized for translation initiation in a particular cell type or tissue,or under a particular set of conditions. In the context of theinvention, “start codon” and “translation initiation codon” refer to thecodon or codons that are used in vivo to initiate translation of an mRNAtranscribed from a gene encoding a nucleic acid target, regardless ofthe sequence(s) of such codons. It is also known in the art that atranslation termination codon (or “stop codon”) of a gene may have oneof three sequences, i.e., 5′-UAA, 5′-UAG and 5′-UGA (the correspondingDNA sequences are 5′-TAA, 5′-TAG and 5′-TGA, respectively).

The terms “start codon region” and “translation initiation codon region”refer to a portion of such an mRNA or gene that encompasses from about25 to about 50 contiguous nucleotides in either direction (i.e., 5′ or3′) from a translation initiation codon. Similarly, the terms “stopcodon region” and “translation termination codon region” refer to aportion of such an mRNA or gene that encompasses from about 25 to about50 contiguous nucleotides in either direction (i.e., 5′ or 3′) from atranslation termination codon. Consequently, the “start codon region”(or “translation initiation codon region”) and the “stop codon region”(or “translation termination codon region”) are all regions which may betargeted effectively with the compositions of the present invention.

The open reading frame (ORF) or “coding region,” which is known in theart to refer to the region between the translation initiation codon andthe translation termination codon, is also a region which may betargeted effectively. Within the context of the present invention, apreferred region is the intragenic region encompassing the translationinitiation or termination codon of the open reading frame (ORF) of agene.

Other target regions include the 5′ untranslated region (5′UTR), knownin the art to refer to the portion of an mRNA in the 5′ direction fromthe translation initiation codon, and thus including nucleotides betweenthe 5′ cap site and the translation initiation codon of an mRNA (orcorresponding nucleotides on the gene), and the 3′ untranslated region(3′UTR), known in the art to refer to the portion of an mRNA in the 3′direction from the translation termination codon, and thus includingnucleotides between the translation termination codon and 3′ end of anmRNA (or corresponding nucleotides on the gene). The 5′ cap site of anmRNA comprises an N7-methylated guanosine residue joined to the 5′-mostresidue of the mRNA via a 5′-5′ triphosphate linkage. The 5′ cap regionof an mRNA is considered to include the 5′ cap structure itself as wellas the first 50 nucleotides adjacent to the cap site. It is alsopreferred to target the 5′ cap region.

Although some eukaryotic mRNA transcripts are directly translated, manycontain one or more regions, known as “introns,” which are excised froma transcript before it is translated. The remaining (and thereforetranslated) regions are known as “exons” and are spliced together toform a continuous mRNA sequence. Targeting splice sites, i.e.,intron-exon junctions or exon-intron junctions, may also be particularlyuseful in situations where aberrant splicing is implicated in disease,or where an overproduction of a particular splice product is implicatedin disease. Aberrant fusion junctions due to rearrangements or deletionsare also preferred target sites. mRNA transcripts produced via theprocess of splicing of two (or more) mRNAs from different gene sourcesare known as “fusion transcripts”. It is also known that introns can beeffectively targeted using antisense oligonucleotides targeted to, forexample, DNA or pre-mRNA.

It is also known in the art that alternative RNA transcripts can beproduced from the same genomic region of DNA. These alternativetranscripts are generally known as “variants”. More specifically,“pre-mRNA variants” are transcripts produced from the same genomic DNAthat differ from other transcripts produced from the same genomic DNA ineither their start or stop position and contain both intronic and exonicsequences.

Upon excision of one or more exon or intron regions, or portions thereofduring splicing, pre-mRNA variants produce smaller “mRNA variants”.Consequently, mRNA variants are processed pre-mRNA variants and eachunique pre-mRNA variant must always produce a unique mRNA variant as aresult of splicing. These mRNA variants are also known as “alternativesplice variants”. If no splicing of the pre-mRNA variant occurs then thepre-mRNA variant is identical to the mRNA variant.

It is also known in the art that variants can be produced through theuse of alternative signals to start or stop transcription and thatpre-mRNAs and mRNAs can possess more that one start codon or stop codon.Variants that originate from a pre-mRNA or mRNA that use alternativestart codons are known as “alternative start variants” of that pre-mRNAor mRNA. Those transcripts that use an alternative stop codon are knownas “alternative stop variants” of that pre-mRNA or mRNA. One specifictype of alternative stop variant is the “polyA variant” in which themultiple transcripts produced result from the alternative selection ofone of the “polyA stop signals” by the transcription machinery, therebyproducing transcripts that terminate at unique polyA sites. Within thecontext of the invention, the types of variants described herein arealso preferred target nucleic acids.

The locations on the target nucleic acid to which the preferredcompositions of the present invention hybridize are hereinbelow referredto as “preferred target segments.” As used herein the term “preferredtarget segment” is defined as at least an 8-nucleobase portion of atarget region that is targeted by the compositions of the invention.While not wishing to be bound by theory, it is presently believed thatthese target segments represent accessible portions of the targetnucleic acid for hybridization.

Exemplary preferred compositions of the invention includeoligonucleotides that comprise at least the 8 consecutive nucleobasesfrom the 5′-terminus of a targeted nucleic acid e.g. a cellular gene ormRNA transcribed from the gene (the remaining nucleobases being aconsecutive stretch of the same oligonucleotide beginning immediatelyupstream of the 5′-terminus of the antisense compound which isspecifically hybridizable to the target nucleic acid and continuinguntil the oligonucleotide contains from about 8 to about 80nucleobases). Similarly preferred compositions of the invention arerepresented by oligonucleotide sequences that comprise at least the 8consecutive nucleobases from the 3′-terminus of one of the illustrativepreferred antisense compounds (the remaining nucleobases being aconsecutive stretch of the same oligonucleotide beginning immediatelydownstream of the 3′-terminus of the antisense compound which isspecifically hybridizable to the target nucleic acid and continuinguntil the oligonucleotide contains from about 8 to about 80nucleobases). One having skill in the art armed with the preferredcompositions of the invention illustrated herein will be able, withoutundue experimentation, to identify further preferred antisensecompounds.

Once one or more target regions, segments or sites have been identified,compositions of the invention are chosen which are sufficientlycomplementary to the target, i.e., hybridize sufficiently well and withsufficient specificity, to give the desired effect.

In accordance with one embodiment of the present invention, a series ofpreferred compositions of the invention can be designed for a specifictarget or targets. The ends of the strands may be blunt or modified bythe addition of one or more natural or modified nucleobases to form anoverhang. The sense strand of the duplex is then designed andsynthesized as the complement of the antisense strand and may alsocontain modifications or additions to either terminus. For example, inone embodiment, both strands of the duplex would be complementary overthe central nucleobases, each optionally having overhangs at one or bothtermini.

For example, a duplex comprising an antisense oligonucleotide having thesequence CGAGAGGCGGACGGGACCG (SEQ ID NO.: 1) and having a two-nucleobaseoverhang of deoxythymidine(dT) would have the following structure:

SEQ ID NO.     cgagaggcggacgggaccgdTdT Antisense Strand 2    ||||||||||||||||||| dTdTgctctccgcctgccctggc Complement Strand 3or could be blunt ended excluding the deoxythymi- dine (dT's):    cgagaggcggacgggaccg Antisense Strand 1     |||||||||||||||||||    gctctccgcctgccctggc Complement Strand 4

RNA strands of the duplex can be synthesized by methods disclosed hereinor purchased from various RNA synthesis companies such as for exampleDharmacon Research Inc., (Lafayette, Colo.). Once synthesized, thecomplementary strands are annealed. The single strands are aliquoted anddiluted to a concentration of 50 uM. Once diluted, 30 uL of each strandis combined with 15 uL of a 5× solution of annealing buffer. The finalconcentration of the buffer is 100 mM potassium acetate, 30 mM HEPES-KOHpH 7.4, and 2 mM magnesium acetate. The final volume is 75 uL. Thissolution is incubated for 1 minute at 90° C. and then centrifuged for 15seconds. The tube is allowed to sit for 1 hour at 37° C. at which timethe dsRNA duplexes are used in experimentation. The final concentrationof the dsRNA compound is 20 uM. This solution can be stored frozen (−20°C.) and freeze-thawed up to 5 times.

Once prepared, the desired synthetic complexes of duplexs are evaluatedfor their ability to modulate target expression. When cells reach 80%confluency, they are treated with synthetic duplexs comprising at leastone oligonucleotide of the invention. For cells grown in 96-well plates,wells are washed once with 200 μL OPTI-MEM-1 reduced-serum medium (GibcoBRL) and then treated with 130μL of OPTI-MEM-1 containing 12 μg/mLLIPOFECTIN (Gibco BRL) and the desired dsRNA compound at a finalconcentration of 200 nM. After 5 hours of treatment, the medium isreplaced with fresh medium. Cells are harvested 16 hours aftertreatment, at which time RNA is isolated and target reduction measuredby RT-PCR.

In a further embodiment, the “preferred target segments” identifiedherein may be employed in a screen for additional oligomeric compoundsthat modulate the expression of a target. “Modulators” are thoseoligomeric compounds that decrease or increase the expression of anucleic acid molecule encoding a target and which comprise at least an8-nucleobase portion which is complementary to a preferred targetsegment. The screening method comprises the steps of contacting apreferred target segment of a nucleic acid molecule encoding a targetwith one or more candidate modulators, and selecting for one or morecandidate modulators which decrease or increase the expression of anucleic acid molecule encoding a target. Once it is shown that thecandidate modulator or modulators are capable of modulating (e.g. eitherdecreasing or increasing) the expression of a nucleic acid moleculeencoding a target, the modulator may then be employed in furtherinvestigative studies of the function of a target, or for use as aresearch, diagnostic, or therapeutic agent in accordance with thepresent invention.

Hybridization

In the context of this invention, “hybridization” occurs when twosequences come together with enough base complementarity to form adouble stranded region. The source of the two sequences can be syntheticor native and can occur in a single strand when the strand has regionsof self complementarity. In the present invention, the preferredmechanism of pairing involves hydrogen bonding, which may beWatson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding, betweencomplementary nucleoside or nucleotide bases (nucleobases) of thestrands of oligonucleotides or between an oligonucleotide and a targetnucleic acid. For example, adenine and thymine are complementarynucleobases which pair through the formation of hydrogen bonds.Hybridization can occur under varying circumstances.

Compositions of the present invention are specifically hybridizable whenbinding to a target nucleic acid interferes with the normal function ofthe target nucleic acid and causes a loss of activity, and there is asufficient degree of complementarity to avoid non-specific binding tonon-target nucleic acid sequences under conditions in which specificbinding is desired, i.e., under physiological conditions in the case ofin vivo assays or therapeutic treatment, and under conditions in whichassays are performed in the case of in vitro assays.

In the present invention the phrase “stringent hybridization conditions”or “stringent conditions” refers to conditions under which compositionsof the invention will hybridize to its target sequence, but to a minimalnumber of other sequences. Stringent conditions are sequence-dependentand will vary with different circumstances and in the context of thisinvention, “stringent conditions” under which oligomeric compoundshybridize to a target sequence are determined by the nature andcomposition of the oligomeric compounds and the assays in which they arebeing investigated.

“Complementary,” as used herein, refers to the capacity for precisepairing of two nucleobases regardless of where the two are located. Forexample, if a nucleobase at a certain position of an oligonucleotide iscapable of hydrogen bonding with a nucleobase at a certain position of atarget nucleic acid, the target nucleic acid being a DNA, RNA, oroligonucleotide molecule, then the position of hydrogen bonding betweenthe oligonucleotide and the target nucleic acid is considered to be acomplementary position. The oligonucleotide and the further DNA, RNA, oroligonucleotide molecule are complementary to each other when asufficient number of complementary positions in each molecule areoccupied by nucleobases which can hydrogen bond with each other. Thus,“specifically hybridizable” and “complementary” are terms which are usedto indicate a sufficient degree of precise pairing or complementarityover a sufficient number of nucleobases such that stable and specificbinding occurs between the oligonucleotide and a target nucleic acid.

It is understood in the art that the sequence of an oligomeric compoundneed not be 100% complementary to that of its target nucleic acid to bespecifically hybridizable. Moreover, an oligmeric compound may hybridizeover one or more segments such that intervening or adjacent segments arenot involved in the hybridization event (e.g., a loop structure orhairpin structure). It is preferred that the oligmeric compounds of thepresent invention comprise at least 70% sequence complementarity to atarget region within the target nucleic acid, more preferably that theycomprise 90% sequence complementarity and even more preferably comprise95% sequence complementarity to the target region within the targetnucleic acid sequence to which they are targeted. For example, anoligmeric compound in which 18 of 20 nucleobases are complementary to atarget region, and would therefore specifically hybridize, wouldrepresent 90 percent complementarity. In this example, the remainingnoncomplementary nucleobases may be clustered or interspersed withcomplementary nucleobases and need not be contiguous to each other or tocomplementary nucleobases. As such, an oligmeric compound which is 18nucleobases in length having 4 (four) noncomplementary nucleobases whichare flanked by two regions of complete complementarity with the targetnucleic acid would have 77.8% overall complementarity with the targetnucleic acid and would thus fall within the scope of the presentinvention. Percent complementarity of an oligmeric compound with aregion of a target nucleic acid can be determined routinely using BLASTprograms (basic local alignment search tools) and PowerBLAST programsknown in the art (Altschul et al., J. Mol. Biol., 1990, 215, 403-410;Zhang and Madden, Genome Res., 1997, 7, 649-656).

Screening and Target Validation

In a further embodiment, “preferred target segments” may be employed ina screen for additional oligmeric compounds that modulate the expressionof a selected protein. “Modulators” are those oligmeric compounds thatdecrease or increase the expression of a nucleic acid molecule encodinga protein and which comprise at least an 8-nucleobase portion which iscomplementary to a preferred target segment. The screening methodcomprises the steps of contacting a preferred target segment of anucleic acid molecule encoding a protein with one or more candidatemodulators, and selecting for one or more candidate modulators whichdecrease or increase the expression of a nucleic acid molecule encodinga protein. Once it is shown that the candidate modulator or modulatorsare capable of modulating (e.g. either decreasing or increasing) theexpression of a nucleic acid molecule encoding a peptide, the modulatormay then be employed in further investigative studies of the function ofthe peptide, or for use as a research, diagnostic, or therapeutic agentin accordance with the present invention.

The preferred target segments of the present invention may also becombined with their respective complementary oligmeric compounds of thepresent invention to form stabilized double-stranded (duplexed)oligmeric compound with oligonucleotides being preferred. Such doublestranded oligonucleotide moieties have been shown in the art to modulatetarget expression and regulate translation as well as RNA processsingvia an antisense mechanism. Moreover, the double-stranded moieties maybe subject to chemical modifications (Fire et al., Nature, 1998, 391,806-811; Timmons and Fire, Nature 1998, 395, 854; Timmons et al., Gene,2001, 263, 103-112; Tabara et al., Science, 1998, 282, 430-431;Montgomery et al., Proc. Natl. Acad. Sci. USA, 1998, 95, 15502-15507;Tuschl et al., Genes Dev., 1999, 13, 3191-3197; Elbashir et al., Nature,2001, 411, 494-498; Elbashir et al., Genes Dev. 2001, 15, 188-200). Forexample, such double-stranded moieties have been shown to inhibit thetarget by the classical hybridization of antisense strand of the duplexto the target, thereby triggering enzymatic degradation of the target(Tijsterman et al., Science, 2002, 295, 694-697).

The compositions of the present invention can also be applied in theareas of drug discovery and target validation. The present inventioncomprehends the use of the compositions and preferred targets identifiedherein in drug discovery efforts to elucidate relationships that existbetween proteins and a disease state, phenotype, or condition. Thesemethods include detecting or modulating a target peptide comprisingcontacting a sample, tissue, cell, or organism with the compositions ofthe present invention, measuring the nucleic acid or protein level ofthe target and/or a related phenotypic or chemical endpoint at some timeafter treatment, and optionally comparing the measured value to anon-treated sample or sample treated with a further oligonucleotide ofthe invention. These methods can also be performed in parallel or incombination with other experiments to determine the function of unknowngenes for the process of target validation or to determine the validityof a particular gene product as a target for treatment or prevention ofa particular disease, condition, or phenotype.

Effect of nucleoside modifications on RNAi activity is evaluatedaccording to existing literature (Elbashir et al., Nature (2001), 411,494-498; Nishikura et al., Cell (2001), 107, 415-416; and Bass et al.,Cell (2000), 101, 235-238.)

Kits, Research Reagents, Diagnostics, and Therapeutics

The compositions of the present invention can be utilized fordiagnostics, therapeutics, prophylaxis and as research reagents andkits. Furthermore, compositions of the present invention, which are ableto inhibit gene expression with exquisite specificity, can be used bythose of ordinary skill to elucidate the function of particular genes orto distinguish between functions of various members of a biologicalpathway.

For use in kits and diagnostics, the compositions of the presentinvention, either alone or in combination with other oligonucleotides ortherapeutics, can be used as tools in differential and/or combinatorialanalyses to elucidate expression patterns of a portion or the entirecomplement of genes expressed within cells and tissues.

As one nonlimiting example, expression patterns within cells or tissuestreated with one or more compositions of the present invention arecompared to untreated control cells or tissues and the patterns producedare analyzed for differential levels of gene expression as they pertain,for example, to disease association, signaling pathway, cellularlocalization, expression level, size, structure or function of the genesexamined. These analyses can be performed on stimulated or unstimulatedcells and in the presence or absence of other compounds and oroligonucleotides that affect expression patterns.

Examples of methods of gene expression analysis known in the art includeDNA arrays or microarrays (Brazma and Vilo, FEBS Lett., 2000, 480,17-24; Celis, et al., FEBS Lett., 2000, 480, 2-16), SAGE (serialanalysis of gene expression)(Madden, et al., Drug Discov. Today, 2000,5, 415-425), READS (restriction enzyme amplification of digested cDNAs)(Prashar and Weissman, Methods Enzymol., 1999, 303, 258-72), TOGA (totalgene expression analysis) (Sutcliffe, et al., Proc. Natl. Acad. Sci.U.S.A., 2000, 97, 1976-81), protein arrays and proteomics (Celis, etal., FEBS Lett., 2000, 480, 2-16; Jungblut, et al., Electrophoresis,1999, 20, 2100-10), expressed sequence tag (EST) sequencing (Celis, etal., FEBS Lett., 2000, 480, 2-16; Larsson, et al., J. Biotechnol., 2000,80, 143-57), subtractive RNA fingerprinting (SuRF) (Fuchs, et al., Anal.Biochem., 2000, 286, 91-98; Larson, et al., Cytometry, 2000, 41,203-208), subtractive cloning, differential display (DD) (Jurecic andBelmont, Curr. Opin. Microbiol., 2000, 3, 316-21), comparative genomichybridization (Carulli, et al., J. Cell Biochem. Suppl., 1998, 31,286-96), FISH (fluorescent in situ hybridization) techniques (Going andGusterson, Eur. J. Cancer, 1999, 35, 1895-904) and mass spectrometrymethods (To, Comb. Chem. High Throughput Screen, 2000, 3, 235-41).

The compositions of the present invention are useful for research anddiagnostic applications. In one aspect of the present invention thecompositions are useful for research and diagnostics in applicationsthat involve the hybridization of compositions to nucleic acids encodingproteins. For example, oligomeric compounds that are shown to hybridizewith such efficiency and under such conditions as disclosed herein as tobe effective protein inhibitors will also be effective primers or probesunder conditions favoring gene amplification or detection, respectively.These primers and probes are useful in methods requiring the specificdetection of nucleic acid molecules encoding proteins and in theamplification of the nucleic acid molecules for detection or for use infurther studies. Hybridization of the antisense oligonucleotides,particularly the primers and probes, of the invention with a nucleicacid can be detected by means known in the art. Such means may includeconjugation of an enzyme to the oligonucleotide, radiolabelling of theoligonucleotide or any other suitable detection means. Kits using suchdetection means for detecting the level of selected proteins in a samplemay also be prepared.

The specificity and sensitivity of antisense methodologies is alsoharnessed by those of skill in the art for therapeutic uses. Antisenseoligonucleotides have been employed as therapeutic moieties in thetreatment of disease states in animals, including humans. Antisenseoligonucleotide drugs, including ribozymes, have been safely andeffectively administered to humans and numerous clinical trials arepresently underway. It is thus established that antisenseoligonucleotides can be useful therapeutic modalities that can beconfigured to be useful in treatment regimes for the treatment of cells,tissues and animals, especially humans.

For therapeutics, an animal, preferably a human, suspected of having adisease or disorder which can be treated by modulating the expression ofa selected protein is treated by administering compositions inaccordance with this invention. For example, in one non-limitingembodiment, the methods comprise the step of administering to the animalin need of treatment, a therapeutically effective amount of a proteininhibitor. The protein inhibitors of the present invention effectivelyinhibit the activity of the protein or inhibit the expression of theprotein. In one embodiment, the activity or expression of a protein inan animal is inhibited by about 10%. Preferably, the activity orexpression of a protein in an animal is inhibited by about 30%. Morepreferably, the activity or expression of a protein in an animal isinhibited by 50% or more.

For example, the reduction of the expression of a protein may bemeasured in serum, adipose tissue, liver or any other body fluid, tissueor organ of the animal. Preferably, the cells contained within thefluids, tissues or organs being analyzed contain a nucleic acid moleculeencoding a protein and/or the protein itself.

The compositions of the present invention can be utilized inpharmaceutical compositions by adding an effective amount to a suitablepharmaceutically acceptable diluent or carrier. Use of the compositionsand methods of the invention may also be useful prophylactically.

Formulations

The compositions of the present invention may also be admixed,encapsulated, conjugated or otherwise associated with other molecules,molecule structures or mixtures of compounds, as for example, liposomes,receptor-targeted molecules, oral, rectal, topical or otherformulations, for assisting in uptake, distribution and/or absorption.

Representative United States patents that teach the preparation of suchuptake, distribution and/or absorption-assisting formulations include,but are not limited to, U.S. Pat. Nos.: 5,108,921; 5,354,844; 5,416,016;5,459,127; 5,521,291; 5,543,158; 5,547,932; 5,583,020; 5,591,721;4,426,330; 4,534,899; 5,013,556; 5,108,921; 5,213,804; 5,227,170;5,264,221; 5,356,633; 5,395,619; 5,416,016; 5,417,978; 5,462,854;5,469,854; 5,512,295; 5,527,528; 5,534,259; 5,543,152; 5,556,948;5,580,575; and 5,595,756, each of which is herein incorporated byreference.

The compositions of the present invention encompass any pharmaceuticallyacceptable salts, esters, or salts of such esters, or any other compoundwhich, upon administration to an animal, including a human, is capableof providing (directly or indirectly) the biologically active metaboliteor residue thereof. Accordingly, for example, the disclosure is alsodrawn to prodrugs and pharmaceutically acceptable salts of thecompositions of the invention, pharmaceutically acceptable salts of suchprodrugs, and other bioequivalents. The term “prodrug” indicates atherapeutic agent that is prepared in an inactive form that is convertedto an active form (i.e., drug) within the body or cells thereof by theaction of endogenous enzymes or other chemicals and/or conditions. Inparticular, prodrug versions of the compositions of the invention areprepared as SATE [(S-acetyl-2-thioethyl) phosphate] derivativesaccording to the methods disclosed in WO 93/24510 to Gosselin et al.,published Dec. 9, 1993 or in WO 94/26764 and U.S. Pat. No. 5,770,713 toImbach et al.

The term “pharmaceutically acceptable salts” refers to physiologicallyand pharmaceutically acceptable salts of the compositions of theinvention: i.e., salts that retain the desired biological activity ofthe parent compound and do not impart undesired toxicological effectsthereto. For oligonucleotides, preferred examples of pharmaceuticallyacceptable salts and their uses are further described in U.S. Pat. No.6,287,860, which is incorporated herein in its entirety.

The present invention also includes pharmaceutical compositions andformulations which include the compositions of the present invention.The pharmaceutical compositions of the present invention may beadministered in a number of ways depending upon whether local orsystemic treatment is desired and upon the area to be treated.Administration may be topical (including ophthalmic and to mucousmembranes including vaginal and rectal delivery), pulmonary, e.g., byinhalation or insufflation of powders or aerosols, including bynebulizer; intratracheal, intranasal, epidermal and transdermal), oralor parenteral. Parenteral administration includes intravenous,intraarterial, subcutaneous, intraperitoneal or intramuscular injectionor infusion; or intracranial, e.g., intrathecal or intraventricular,administration. Oligonucleotides with at least one 2′-O-methoxyethylmodification are believed to be particularly useful for oraladministration. Pharmaceutical compositions and formulations for topicaladministration may include transdermal patches, ointments, lotions,creams, gels, drops, suppositories, sprays, liquids and powders.Conventional pharmaceutical carriers, aqueous, powder or oily bases,thickeners and the like may be necessary or desirable. Coated condoms,gloves and the like may also be useful.

The pharmaceutical formulations of the present invention, which mayconveniently be presented in unit dosage form, may be prepared accordingto conventional techniques well known in the pharmaceutical industry.Such techniques include the step of bringing into association the activeingredients with the pharmaceutical carrier(s) or excipient(s). Ingeneral, the formulations are prepared by uniformly and intimatelybringing into association the active ingredients with liquid carriers orfinely divided solid carriers or both, and then, if necessary, shapingthe product.

The compositions of the present invention may be formulated into any ofmany possible dosage forms such as, but not limited to, tablets,capsules, gel capsules, liquid syrups, soft gels, suppositories, andenemas. The compositions of the present invention may also be formulatedas suspensions in aqueous, non-aqueous or mixed media. Aqueoussuspensions may further contain substances which increase the viscosityof the suspension including, for example, sodium carboxymethylcellulose,sorbitol and/or dextran. The suspension may also contain stabilizers.

Pharmaceutical compositions of the present invention include, but arenot limited to, solutions, emulsions, foams and liposome-containingformulations. The pharmaceutical compositions and formulations of thepresent invention may comprise one or more penetration enhancers,carriers, excipients or other active or inactive ingredients.

Emulsions are typically heterogenous systems of one liquid dispersed inanother in the form of droplets usually exceeding 0.1 μm in diameter.Emulsions may contain additional components in addition to the dispersedphases, and the active drug which may be present as a solution in eitherthe aqueous phase, oily phase or itself as a separate phase.Microemulsions are included as an embodiment of the present invention.Emulsions and their uses are well known in the art and are furtherdescribed in U.S. Pat. No. 6,287,860, which is incorporated herein inits entirety.

Formulations of the present invention include liposomal formulations. Asused in the present invention, the term “liposome” means a vesiclecomposed of amphiphilic lipids arranged in a spherical bilayer orbilayers. Liposomes are unilamellar or multilamellar vesicles which havea membrane formed from a lipophilic material and an aqueous interiorthat contains the composition to be delivered. Cationic liposomes arepositively charged liposomes which are believed to interact withnegatively charged DNA molecules to form a stable complex. Liposomesthat are pH-sensitive or negatively-charged are believed to entrap DNArather than complex with it. Both cationic and noncationic liposomeshave been used to deliver DNA to cells.

Liposomes also include “sterically stabilized” liposomes, a term which,as used herein, refers to liposomes comprising one or more specializedlipids that, when incorporated into liposomes, result in enhancedcirculation lifetimes relative to liposomes lacking such specializedlipids. Examples of sterically stabilized liposomes are those in whichpart of the vesicle-forming lipid portion of the liposome comprises oneor more glycolipids or is derivatized with one or more hydrophilicpolymers, such as a polyethylene glycol (PEG) moiety. Liposomes andtheir uses are further described in U.S. Pat. No. 6,287,860, which isincorporated herein in its entirety.

The pharmaceutical formulations and compositions of the presentinvention may also include surfactants. The use of surfactants in drugproducts, formulations and in emulsions is well known in the art.Surfactants and their uses are further described in U.S. Pat. No.6,287,860, which is incorporated herein in its entirety.

In one embodiment, the present invention employs various penetrationenhancers to effect the efficient delivery of nucleic acids,particularly oligonucleotides. In addition to aiding the diffusion ofnon-lipophilic drugs across cell membranes, penetration enhancers alsoenhance the permeability of lipophilic drugs. Penetration enhancers maybe classified as belonging to one of five broad categories, i.e.,surfactants, fatty acids, bile salts, chelating agents, andnon-chelating non-surfactants. Penetration enhancers and their uses arefurther described in U.S. Pat. No. 6,287,860, which is incorporatedherein in its entirety.

One of skill in the art will recognize that formulations are routinelydesigned according to their intended use, i.e. route of administration.

Preferred formulations for topical administration include those in whichthe compositions of the invention are in admixture with a topicaldelivery agent such as lipids, liposomes, fatty acids, fatty acidesters, steroids, chelating agents and surfactants. Preferred lipids andliposomes include neutral (e.g. dioleoylphosphatidyl DOPE ethanolamine,dimyristoylphosphatidyl choline DMPC, di stearolyphosphatidyl choline)negative (e.g. dimyristoylphosphatidyl glycerol DMPG) and cationic (e.g.dioleoyltetramethylaminopropyl DOTAP and dioleoylphosphatidylethanolamine DOTMA).

For topical or other administration, compositions of the presentinvention may be encapsulated within liposomes or may form complexesthereto, in particular to cationic liposomes. Alternatively,compositions of the present invention may be complexed to lipids, inparticular to cationic lipids. Preferred fatty acids and esters,pharmaceutically acceptable salts thereof, and their uses are furtherdescribed in U.S. Pat. No. 6,287,860, which is incorporated herein inits entirety. Topical formulations are described in detail in U.S.patent application Ser. No. 09/315,298 filed on May 20, 1999, which isincorporated herein by reference in its entirety.

Compositions and formulations for oral administration include powders orgranules, microparticulates, nanoparticulates, suspensions or solutionsin water or non-aqueous media, capsules, gel capsules, sachets, tabletsor minitablets. Thickeners, flavoring agents, diluents, emulsifiers,dispersing aids or binders may be desirable. Preferred oral formulationsare those in which compositions of the invention are administered inconjunction with one or more penetration enhancers surfactants andchelators. Preferred surfactants include fatty acids and/or esters orsalts thereof, bile acids and/or salts thereof. Preferred bileacids/salts and fatty acids and their uses are further described in U.S.Pat. No. 6,287,860, which is incorporated herein in its entirety. Alsopreferred are combinations of penetration enhancers, for example, fattyacids/salts in combination with bile acids/salts. A particularlypreferred combination is the sodium salt of lauric acid, capric acid andUDCA. Further penetration enhancers include polyoxyethylene-9-laurylether, polyoxyethylene-20-cetyl ether. Compositions of the presentinvention may be delivered orally, in granular form including sprayeddried particles, or complexed to form micro or nanoparticles.Oligonucleotide complexing agents and their uses are further describedin U.S. Pat. No. 6,287,860, which is incorporated herein in itsentirety. Oral formulations for oligonucleotides and their preparationare described in detail in U.S. applications Ser. No. 09/108,673 (filedJul. 1, 1998), Ser. No. 09/315,298 (filed May 20, 1999) and Ser. No.10/071,822, filed February 8, 2002, each of which is incorporated hereinby reference in their entirety.

Compositions and formulations for parenteral, intrathecal orintraventricular administration may include sterile aqueous solutionsthat may also contain buffers, diluents and other suitable additivessuch as, but not limited to, penetration enhancers, carrier compoundsand other pharmaceutically acceptable carriers or excipients.

Certain embodiments of the invention provide pharmaceutical compositionscontaining one or more of the compositions of the present invention andone or more other chemotherapeutic agents which function by anon-antisense mechanism. Examples of such chemo-therapeutic agentsinclude but are not limited to cancer chemotherapeutic drugs such asdaunorubicin, daunomycin, dactinomycin, doxorubicin, epirubicin,idarubicin, esorubicin, bleomycin, mafosfamide, ifosfamide, cytosinearabinoside, bis-chloroethylnitrosurea, busulfan, mitomycin C,actinomycin D, mithramycin, prednisone, hydroxyprogesterone,testosterone, tamoxifen, dacarbazine, procarbazine, hexamethylmelamine,pentamethylmelamine, mitoxantrone, amsacrine, chlorambucil,methylcyclohexylnitrosurea, nitrogen mustards, melphalan,cyclophosphamide, 6-mercaptopurine, 6-thioguanine, cytarabine,5-azacytidine, hydroxyurea, deoxycoformycin,4-hydroxyperoxycyclophosphoramide, 5-fluorouracil (5-FU),5-fluorodeoxyuridine (5-FUdR), methotrexate (MTX), colchicine, taxol,vincristine, vinblastine, etoposide (VP-16), trimetrexate, irinotecan,topotecan, gemcitabine, teniposide, cisplatin and diethylstilbestrol(DES). When used with the compositions of the invention, suchchemotherapeutic agents may be used individually (e.g., 5-FU andoligonucleotide), sequentially (e.g., 5-FU and oligonucleotide for aperiod of time followed by MTX and oligonucleotide), or in combinationwith one or more other such chemotherapeutic agents (e.g., 5-FU, MTX andoligonucleotide, or 5-FU, radiotherapy and oligonucleotide).Anti-inflammatory drugs, including but not limited to nonsteroidalanti-inflammatory drugs and corticosteroids, and antiviral drugs,including but not limited to ribivirin, vidarabine, acyclovir andganciclovir, may also be combined in compositions of the invention.Combinations of compositions of the invention and other non-antisensedrugs are also within the scope of this invention. One or morecompositions of the invention can be used in combination with othertherapeutic agents to create a cocktail as is currently the strategy forcertain viral infections.

In another related embodiment, therapeutically effective combinationtherapies may comprise the use of two or more oligonucleotides and orcompositions of the present invention wherein the multiple compositionsare targeted to a single or multiple nucleic acid targets. Numerousexamples of antisense oligonucleotides are known in the art. Two or morecombined compounds may be used together or sequentially

Dosing

The formulation of therapeutic compositions and their subsequentadministration (dosing) is believed to be within the skill of those inthe art. Dosing is dependent on severity and responsiveness of thedisease state to be treated, with the course of treatment lasting fromseveral days to several months, or until a cure is effected or adiminution of the disease state is achieved. Optimal dosing schedulescan be calculated from measurements of drug accumulation in the body ofthe patient. Persons of ordinary skill can easily determine optimumdosages, dosing methodologies and repetition rates. Optimum dosages mayvary depending on the relative potency of individual oligonucleotides,and can generally be estimated based on EC₅₀s found to be effective inin vitro and in vivo animal models. In general, dosage is from 0.01 ugto 100 g per kg of body weight, and may be given once or more daily,weekly, monthly or yearly, or even once every 2 to 20 years. Persons ofordinary skill in the art can easily estimate repetition rates fordosing based on measured residence times and concentrations of the drugin bodily fluids or tissues. Following successful treatment, it may bedesirable to have the patient undergo maintenance therapy to prevent therecurrence of the disease state, wherein the oligonucleotide isadministered in maintenance doses, ranging from 0.01 ug to 100 g per kgof body weight, once or more daily, to once every 20 years.

While the present invention has been described with specificity inaccordance with certain of its preferred embodiments, the followingexamples serve only to illustrate the invention and are not intended tolimit the same.

EXAMPLE 1

Alternating 2′-O-Methyl siRNA's Targeting PTEN

A dose response was performed in the PTEN system to look at positionaleffects of alternating 2′-O-methyl constructs in asRNA and siRNAconstructs.

SEQ ID NO/ISIS NO SEQUENCES 5′-3′  8/3354545′-P-UUUGUCUCUGGUCCUUACUU (P = S, antisense)  9/3354555′-P-UUUGUCUCUGGUCCUUACUU (P = S, antisense) 10/3354565′-P-UUUGUCUCUGGUCCUUACUU (P = O, antisense) 11/3354575′-P-UUUGUCUCUGGUCCUUACUU (P = O, antisense) 12/3039125′-P-UUUGUCUCUGGUCCUUACUU (P = S, antisense) 13/308746AAGUAAGGACCAGAGACAAA (P = O, sense) 14/335452 AAGUAAGGACCAGAGACAAA (P =O, sense) 15/335453 AAGUAAGGACCAGAGACAAA (P = O, sense) Underlined =2′-O-methyl and 5′-P-is a 5′-phosphate group.siRNA duplexes (5′, 3′-sense and 3′, 5′-antisense) Activity (150 nm)13/308746 (S, P = O) 5′-AAGUAAGGACCAGAGACAAA-3′ 14.8 12/303912 (AS, P =S) 3′-UUCAUUCCUGGUCUCUGUUU-P-5′ (unmodified standard)siRNA duplexes (5′, 3′-sense and 3′, 5′-antisense) Activity (150 nm)14/335452 (S, P = O) 5′- A A G U A A G G A C C A G A G A C A A A-3′ 8/335454 (AS, P = S) 3′-UUCAUUCCUGGUCUCUGUUU-P-5′ 43.810/335456 (AS, P = O) 3′-UUCAUUCCUGGUCUCUGUUU-P-5′ 41.0 9/335455 (AS, P = S) 3′-UUCAUUCCUGGUCUCUGUUU-P-5′ 53.111/335457 (AS, P = O) 3′-UUCAUUCCUGGUCUCUGUUU-P-5′ 49.715/335453 (S, P = O) 5′-A A G U A A G G A C C A G A G A C A A A -3′ 8/335454 (AS, P = S) 3′-UUCAUUCCUGGUCUCUGUUU-P-5′ 54.310/335456 (AS, P = O) 3′-UUCAUUCCUGGUCUCUGUUU-P-5′ 50.3 9/335455 (AS, P = S) 3′-UUCAUUCCUGGUCUCUGUUU-P-5′ 52.211/335457 (AS, P = O) 3′-UUCAUUCCUGGUCUCUGUUU-P-5′ 52.813/308746 (S, P = O) 5′-AAGUAAGGACCAGAGACAAA-3′  8/335454 (AS, P = S)3′-UUCAUUCCUGGUCUCUGUUU-P-5′ 40.0 10/335456 (AS, P = O)3′-UUCAUUCCUGGUCUCUGUUU-P-5′ 26.3  9/335455 (AS, P = S)3′-UUCAUUCCUGGUCUCUGUUU-P-5′ 56.6 11/335457 (AS, P = O)3′-UUCAUUCCUGGUCUCUGUUU-P-5′ 74.4asRNA single stranded (5′, 3′-sense and 3′, 5′-antisense)Activity (200 nm) 12/303912 (AS, P = S) 3′-UUCAUUCCUGGUCUCUGUUU-P-5′27.9  8/335454 (AS, P = S) 3′-UUCAUUCCUGGUCUCUGUUU-P-5′ 53.510/335456 (AS, P = O) 3′-UUCAUUCCUGGUCUCUGUUU-P-5′ 93.2 9/335455 (AS, P = S) 3′-UUCAUUCCUGGUCUCUGUUU-P-5′ 48.311/335457 (AS, P = O) 3′-UUCAUUCCUGGUCUCUGUUU-P-5′ 89.6 SEQ ID NO:Sequence (5′-3′) 12 UUUGUCUCUGGUCCUUACUU 13 AAGUAAGGACCAGAGACAAA

The asRNA assay was run as a dose response with only the 200 nm doseshown (0, 50, 100 and 200 nm). The siRNA assay was also performed as adose response with only the 150 nm dose shown (20, 40 80, 150 nm).

EXAMPLE 2

Alternating 2′-F siRNA's Targeting PTEN in T-24 cells

A dose response was performed in the PTEN system to look at positionaleffects of alternating 2′-F constructs in asRNA constructs.

SEQ ID NO/ ISIS NO SEQUENCE 13/308746 5′-P-AAG UAA GGA CCA GAG AC AAA-3′(PO, S, RNA) 12/303912 3′-OH-UUC AUU CCU GGU CUC UGU UU-P-5′(PS, AS, RNA) 16/339927 5′-PO-AAG UAA GGA CCA GAG ACA AA-3′(PO, S, deoxy) 17/339923 3′-OH-UTC AUT C ^(m)CU GGT CTC TGT UT-5′-P(PO, AS, deoxy) 18/339928 5′-PO-AAG UAA GGA  ^(m)CCA GAG ACA AA-3′(PO, S, deoxy) 17/339923 3′-OH-UTC AUT C ^(m)CU GGT CTC TGT UT-5′-P(PO, AS, deoxy) 13/308746 5′-PO-AAG UAA GGA CCA GAG ACA AA-3′(PO, S, RNA) 17/339923 3′-OH-UTC AUT C ^(m)CU GGT CTC TGT UT-5′-P(PO, AS, deoxy) 16/339927 5′-PO-AAG UAA GGA CCA GAG ACA AA-3′(PO, S, deoxy) 17/339924 3′-OH-UTC AUT C ^(m)CU GGT CTC TGT UT-5′-P(PS, AS, deoxy) 18/339928 5′-PO-AAG UAA GGA  ^(m)CCA GAG ACA AA-3′(PO, S, deoxy) 19/339924 3′-OH-UTC AUT C ^(m)CU GGT CTC TGT UT-5′-P(PS, AS, deoxy) 13/308746 5′-PO-AAG UAA GGA CCA GAG ACA AA-3′(PO, S, RNA) 19/339924 3′-OH-UTC AUT C ^(m)CU GGT CTC TGT UT-5′-P(PS, AS, deoxy)

Underlined nucleosides are 2′-F modified nucleosides, all othernucleosides are ribonucleosides (RNA) or 2′-deoxyribonucleosides (deoxy)as annotated, PO and PS are phosphodiester and phosphorothioaterespectively, 5′-P is 5′-phosphate, and ^(m)C′s are 5-methyl cytidines.

SEQ ID NO: Sequence (5′-3′) 20 TUTGTCTCTGGUCCTUACTU

The above siRNA constructs were assayed to determine the effects of thefull alternating 2′-F/2′-deoxy antisense strands (PO or PS) as comparedto sense strands having full alternating 2′-F/2′-deoxy (PO). The siRNAconstruct having PO sense and PS antisense strands that are full RNA wasprepared for comparison.

The activities are listed below:

siRNA Activity (% untreated control 150 nM) Construct Sense Antisense308746/303912 16% PO unmodified RNA /PS unmodified RNA 339927/339923 81%PO deoxy alternating 3′-1 /PO deoxy alternating 5′-1 339927/339924 39%PO deoxy alternating 3′-1 /PS deoxy alternating 5′-1 339928/339923 81%PO deoxy alternating 3′-0 /PO deoxy alternating 5′-1 339928/339924 39%PO deoxy alternating 3′-0 /PS deoxy alternating 5′-1 308746/339923 43%PO unmodified RNA /PO deoxy alternating 5′-1 308746/339924 37% POunmodified RNA /PS deoxy alternating 5′-1

The alternating 3′-1 (sense strand) means that the alternating 2′-Fgroups start adjacent to the 3′-nucleoside and 3′-0 means the 2′-Fstarts alternating at the 3′-terminal nucleoside, alternating 5′-1(antisense strand) means that the alternating 2′-F groups start adjacentto the 5′-nucleoside. nucleoside.

EXAMPLE 3

Alternating 2′-F siRNA's Targeting PTEN in T-24 cells

A dose response was performed in the PTEN system to look at positionaleffects of alternating 2′-F constructs in asRNA constructs.

SEQ ID NO/ ISIS NO SEQUENCE 13/308746 5′-P-AAG UAA GGA CCA GAG AC AAA-3′(PO, S, RNA) 12/303912 3′-OH-UUC AUU CCU GGU CUC UGU UU-P-5′(PS, AS, RNA) 16/339927 5′-PO-AAG UAA GGA CCA GAG ACA AA-3′(PO, S, deoxy) 21/339925 3′-OH-TU ^(m)C ATU ^(m)CCT GGU ^(m)CU^(m)C UGU TU- 5′-P (PO, AS, deoxy) 18/339928 5′-PO-AAG UAA GGA ^(m)CCA GAG ACA AA-3′ (PO, S, deoxy) 21/339925 3′-OH-TU^(m)C ATU ^(m)CCT GGU ^(m)CU ^(m)C UGU TU- 5′-P (PO, AS, deoxy)13/308746 5′-PO-AAG UAA GGA CCA GAG ACA AA-3′ (PO, S, RNA) 21/3399253′-OH-TU ^(m)C ATU ^(m)CCT GGU ^(m)CU ^(m)C UGU TU- 5′-P (PO, AS, deoxy)16/339927 5′-PO-AAG UAA GGA CCA GAG ACA AA-3′ (PO, S, deoxy) 21/3399263′-OH-TU ^(m)C ATU ^(m)CCT GGU ^(m)CU ^(m)C UGU TU- 5′-P (PS, AS, deoxy)18/339928 5′-PO-AAG UAA GGA ^(m)CCA GAG ACA AA-3′ (PO, AS, deoxy)21/339926 3′-OH-TU ^(m)C ATU ^(m)CCT GGU ^(m)CU ^(m)C UGU TU-5′-P (PO, S, deoxy) 13/308746 5′-PO-AAG UAA GGA CCA GAG ACA AA-3′(PO, S, RNA) 22/339926 3′-OH-TU ^(m)C ATU ^(m)CCT GGU ^(m)CU^(m)C UGU TU- 5′-P (PS, AS, deoxy)

Underlined nucleosides are 2′-F modified nucleosides, all othernucleosides are ribonucleosides (RNA) or 2′-deoxyribonucleosides (deoxy)as annotated, PO and PS are phosphodiester and phosphorothioaterespectively, 5′-P is 5′-phosphate, and ^(m)C′s are 5-methyl cytidines.

SEQ ID NO: Sequence (5′-3′) 23 UTUGUCUCUGGTCCUTACUT

The above siRNA constructs were assayed to determine the effects of thefull alternating 2′-F/2′-deoxy antisense strands (PO or PS) as comparedto sense strands having full alternating 2′-F/2′-deoxy (PO). The siRNAconstruct having PO sense and PS antisense strands that are full RNA wasprepared for comparison. The register of the antisense strand has beenshifted relative to Example 2 (2′-F is at 5′-0 as opposed to 5′-1).

The activities are listed below:

siRNA Activity (% untreated control 150 nM) Construct Sense Antisense308746/303912 16% PO unmodified RNA /PS unmodified RNA 339927/339925 86%PO deoxy alternating 3′-1 /PO deoxy alternating 5′-0 339927/339926 79%PO deoxy alternating 3′-1 /PS deoxy alternating 5′-0 339928/339925 51%PO deoxy alternating 3′-0 /PO deoxy alternating 5′-0 339928/339926 69%PO deoxy alternating 3′-0 /PS deoxy alternating 5′-0 308746/339925 73%PO unmodified RNA /PO deoxy alternating 5′-0 308746/339926 52% POunmodified RNA /PS deoxy alternating 5′-0

The alternating 3′-1 (sense strand) means that the alternating 2′-Fgroups start adjacent to the 3′-nucleoside and 3′-0 means the 2′-Fstarts alternating at the 3′-terminal nucleoside, alternating 5′-1(antisense strand) means that the alternating 2′-F groups start adjacentto the 5′-nucleoside.

EXAMPLE 4

Alternating 2′-O-Methyl/2′-F siRNA's Targeting PTEN in T-24 cells

A dose response was performed in the PTEN system to look at positionaleffects of alternating 2′-O-Methyl/2′-F siRNA's.

SEQ ID NO/ SEQUENCE (Bold = 2′-F, Underlined = ISIS NO 2′-OCH₃)13/308746 5′-P-AAG UAA GGA CCA GAG AC AAA-3′ (PO, S, RNA) 12/3039123′-OH-UUC AUU CCU GGU CUC UGU UU-P-5′ (PS, AS, RNA) 24/340573 5′-PO-A AG U A A G G A C C A G A G A C A A A-3′ (PO, S) 25/340569 3′-OH-U U C A UU C C U G G U C U C U G U U U-5′-P (PO, AS) 26/340574 5′-PO-A A G U AA G G A C C A G A G A C A A A-3′ (PO, S) 25/340569 3′-OH-U U C A U U C CU G G U C U C U G U U U-5′-P (PO, AS) 13/3087465′-PO-AAG UAA GGA CCA GAG ACA AA-3′ (PO, AS, RNA) 25/340569 3′-OH-U UC A U U C C U G G U C U C U G U U U-5′-P (PO, AS) 24/340573 5′-PO-A AG U A A G G A C C A G A G A C A A A-3′ (PO, S) 27/340570 3′-OH-U U C A UU C C U G G U C U C U G U U U-5′-P (PS, AS) 26/340574 5′-PO-A A G U AA G G A C C A G A G A C A A A-3′ (PO, S) 27/340570 3′-OH-U U C A U U C CU G G U C U C U G U U U-5′-P (PS, AS) 13/3087465′-PO-AAG UAA GGA CCA GAG ACA AA-3′ (PO, AS, RNA) 27/340570 3′-OH-U UC A U U C C U G G U C U C U G U U U-5′-P (PS, AS)

Underlined nucleosides are 2′-OCH3 modified nucleosides, bold are 2′-Fmodified nucleosides, PO and PS are phosphodiester and phosphorothioaterespectively, 5′-P is 5′-phosphate, and ^(m)C′s are 5-methyl cytidines.

The above siRNA constructs were assayed to determine the effects of thefull alternating 2′-0-methyl/2′-F antisense strands (PO or PS) where the5′-terminus of the antisense strands are 2′-F modified nucleosides withthe remaining positions alternating. The sense strands were preparedwith the positioning of the modified nucleosides in both orientationssuch that for each siRNA tested with 2′-0-methyl modified nucleosidesbegining at the the 3′-terminus of the sense strand another identicalsiRNA was prepared with 2′-F modified nucleosides begining at the the3′-terminus of the sense strand. Another way to describe the differencesbetween these two siRNA's is that the register of the sense strand is inboth possible orientations with the register of the antisense strandbeing held constant in one orientation.

The activities are listed below:

siRNA Activity (% untreated control 150 nM) Construct Sense Antisense308746/303912 28% PO unmodified RNA PS unmodified RNA 340574/340569 46%PO (2′-F, 3′-0) PO (2′-F, 5′-0) 340574/340570 62% PO (2′-F, 3′-0) PS(2′-F, 5′-0) 340573/340569 84% PO (2′-O-methyl, 3′-0) PO (2′-F, 5′-0)340573/340570 23% PO (2′-O-methyl, 3′-0) PS (2′-F, 5′-0) 308746/34056923% PO unmodified RNA PO (2′-F, 5′-0) 308746/340570 38% PO unmodifiedRNA PS (2′-F, 5′-0)

Within the alternating motif for this assay the antisense strands wereprepared begining with a 2′-F group at the 5′-terminal nucleoside. Thesense strands were prepared with the alternating motif begining at the3′-terminal nucleoside with either the 2′-F (2′-F, 3′-0) or the2′-O-methyl (2′-0-methyl, 3′-0). The siRNA constructs were prepared withthe internucleoside linkages for the sense strand as full phosphodiesterand the internucleoside linkages for the antisense strands as eitherfull phosphodiester or phosphorothioate.

EXAMPLE 5

Alternating 2′-O-Methyl/2′-F siRNA's Targeting PTEN in T-24 cells

A dose response was performed in the PTEN system to look at positionaleffects of alternating 2′-0-Methyl/2′-F siRNA's.

SEQ ID NO/ SEQUENCE (Bold = 2′-F, Underlined = ISIS NO 2′-OCH₃)13/308746 5′-P-AAG UAA GGA CCA GAG AC AAA-3′ (PO, S, RNA) 12/3039123′-OH-UUC AUU CCU GGU CUC UGU UU-P-5′ (PS, AS, RNA) 24/340573 5′-PO-A AG U A A G G A C C A G A G A C A A A-3′ (PO, S) 28/340571 3′-OH-U U C A UU C C U G G U C U G U U U-5′-P (PO, AS) 26/340574 5′-PO-A A G U A A G GA C C A G A G A C A A A-3′ (PO, S) 28/340571 3′-OH-U U C A U U C C U G GU C U G U U U-5′-P (PO, AS) 13/3087465′-PO-AAG UAA GGA CCA GAG ACA AA-3′ (PO, AS, RNA) 28/340571 3′-OH-U UC A U U C C U G G U C U G U U U-5′-P (PO, AS) 24/340573 5′-PO-A A G U AA G G A C C A G A G A C A A A-3′ (PO, S) 29/340572 3′-OH-U U C A U U C CU G G U C U G U U U-5′-P (PS, AS) 26/340574 5′-PO-A A G U A A G G A C CA G A G A C A A A-3′ (PO, S) 29/340572 3′-OH-U U C A U U C C U G G U C UG U U U-5′-P (PS, AS) 13/308746 5′-PO-AAG UAA GGA CCA GAG ACA AA-3′(PO, AS, RNA) 29/340572 3′-OH-U U C A U U C C U G G U C U G U U U-5′-P(PS, AS)

Underlined nucleosides are 2′-F modified nucleosides, bold are 2′-Fmodified nucleosides, PO and PS are phosphodiester and phosphorothioaterespectively, 5′-P is 5′-phosphate, and ^(m)C′s are 5-methyl cytidines.

The above siRNA constructs were assayed to determine the effects of thefull alternating 2′-0-methyl/2′-F antisense strands (PO or PS) where the5′-terminus of the antisense strands are 2′-0-methyl modifiednucleosides with the remaining positions alternating. The sense strandswere prepared with the positioning of the modified nucleosides in bothorientations such that for each siRNA tested with 2′-O-methyl modifiednucleosides begining at the the 3′-terminus of the sense strand anotheridentical siRNA was prepared with 2′-F modified nucleosides begining atthe the 3′-terminus of the sense strand. Another way to describe thedifferences between these two siRNA's is that the register of the sensestrand is in both possible orientations with the register of theantisense strand being held constant in one orientation.

The activities are listed below:

siRNA Activity (% untreated control 150 nM) Construct Sense Antisense308746/303912 27% PO unmodified RNA PS unmodified RNA 340574/340571 112%PO (2′-F, 3′-0) PO (2′-O-methyl, 5′-0) 340574/340572 81% PO (2′-F, 3′-0)PS (2′-O-methyl, 5′-0) 340573/340571 40% PO (2′-O-methyl, 3′-0) PO(2′-O-methyl, 5′-0) 340573/340572 71% PO (2′-O-methyl, 3′-0) PS(2′-O-methyl, 5′-0) 308746/340571 46% PO unmodified RNA PO (2′-O-methyl,5′-0) 308746/340572 44% PO unmodified RNA PS (2′-O-methyl, 5′-0)

Within the alternating motif for this assay the antisense strands wereprepared begining with a 2′-F group at the 5′-terminal nucleoside. Thesense strands were prepared with the alternating motif begining at the3′-terminal nucleoside with either the 2′-F (2′-F, 3′-0) or the2′-O-methyl (2′-O(-methyl, 3′-0). The siRNA constructs were preparedwith the internucleoside linkages for the sense strand as fullphosphodiester and the internucleoside linkages for the antisensestrands as either full phosphodiester or phosphorothioate.

EXAMPLE 6

Double Stranded Alternating Constructs

A number of double stranded constructs were also assayed in HeLa cells.The constructs and activities are shown below:

SEQ ID NO/ ISIS NO SEQUENCES 5′-3′  12/3039125′-PO-UU UGU CUC UGG UCC UUA CUU-3′ (AS, PS) 124/3087465′-PO-AAG TAA GGA CCA GAG ACA AA-3′ (S, PO) 125/3354525′-PO-AAG TAA GGA CCA GAG ACA AA-3′ (PO, 2′-OMe)  15/3354535′-PO-AAG UAA GGA CCA GAG ACA AA-3′ (PO, 2′-OMe)   8/3354545′-PO-UU UGU CUC UGG UCC UUA CUU-3′ (PS, 2′-OMe)   9/3354555′-PO-UU UGU CUC UGG UCC UUA CUU-3′ (PS, 2′-OMe)  10/3354565′-PO-UU UGU CUC UGG UCC UUA CUU-3′ (PO, 2′-OMe)  11/3354575′-PO-UU UGU CUC UGG UCC UUA CUU-3′3′ (PO, 2′-OMe)  17/3399235′-PO-TU TGT CTC TGG U ^(m)CC TUA CTU-3′ (PO, 2′-F/2′-H)  19/3399245′-PO-TU TGT CTC TGG U ^(m)CC TUA CTU-3′ (PS, 2′-F/2′-H)  21/3399255′-PO-UT UGU ^(m)CU ^(m)C UGG TC ^(m)C UTA ^(m)CUT-3′ (PO, 2′-F/2′-H) 22/339926 5′-PO-UT UGU ^(m)CU ^(m)C UGG TC ^(m)C UTA ^(m)CUT-3′(PS, 2′-F/2′-H) 126/339927 5′-PO-AAG TAA GGA ^(m)CCA GAG ACA AA-3′(PS, 2′-F/2′-H) 127/339928 5′-PO-AAG UAA GGA C ^(m)CA GAG A ^(m)CA AA-3′(PO, 2′-F/2′-H)  25/340569 5′-PO-UUU GUC UCU GGU CCU UAC UU-3′(PO, 2′-F/2′-OMe)  27/340570 5′-PO-UUU GUC UCU GGU CCU UAC UU-3′(PS, 2′-F/2′-OMe) 128/340571 5′-PO-UUU GUC UCU GGU CCU UAC UU-3′(PO, 2′-F/2′-OMe) 129/340572 5′-PO-UUU GUC UCU GGU CCU UAC UU-3′(PS, 2′-F/2′-OMe) 130/340573 5′-PO-AAG UAA GGA CCA GAG ACA AA-3′(PO, 2′-F/2′-OMe) 131/340574 5′-PO-AAG UAA GGA CCA GAG ACA AA-3′(PO, 2′-F/2′-OMe)  30/344217 5′-PO-UUU GUC UCU GGU CCU UAC UU-3′(PO, 2′-F)  31/344218 5′-PO-UUU GUC UCU GGU CCU UAC UU-3′ (PS, 2′-F) 32/344219 5′-PO-UUU GUC UCU GGU CCU UAC UU-3′ (PO, 2′-F)  33/3442205′-PO-UUU GUC UCU GGU CCU UAC UU-3′ (PS, 2′-F)  34/3442215′-PO-AAG UAA GGA CCA GAG ACA AA-3′ (PO, 2′-F)  35/3442225′-PO-AAG UAA GGA CCA GAG ACA AA-3′ (PO, 2′-F)

The particular constructs and their activities are shown below:

Double stranded construct Activity Antisense Sense % UTC (dose; nM) IC50(nM) 303912 308746 24 (100) 2 339923 339927 52 (100) 339923 339928 51(100) 100 339923 308746 41 (100) 12 339924 339927 43 (100) 56 339924339928 34 (100) 51 339924 308746 46 (100) 77 339925 339927 78 (100)339925 339928 91 (100) 339925 308746 65 (100) 339926 339927 53 (100)339926 339928 47 (100) 339926 308746 34 (100) 67 335454 335452 52 (11)19 335454 335453 58 (11) 67 335454 308746 63 (11) 34 335455 335452 59(11) 30 335455 335453 54 (11) 15 335455 308746 69 (100) 335456 335452 45(11) 3 335456 335453 51 (11) 21 335456 308746 38 (11) 1 335457 335452 56(100) 335457 335453 52 (11) 14 335457 308746 52 (100) 340569 340573 67(15) 340569 340574 35 (15) 4 340569 308746 19 (15) 0.2 340570 340573 25(15) 3 340570 340574 77 (15) 92 340570 308746 52 (15) 23 340571 34057332 (15) 4 340571 340574 84 (15) 340571 308746 38 (15) 4 340572 340573 64(15) 340572 340574 71 (15) 340572 308746 51 (15) 0.7 344217 344222 23(15) 0.7 344217 308746 22 (15) 0.8 344218 344221 28 (15) 3 344218 34422228 (15) 5 344218 308746 28 (15) 3 344219 344221 44 (15) 6 344219 34422240 (15) 6 344219 308746 31 (15) 2 344220 344221 47 (15) 33 344220 34422252 (15) 55 344220 308746 44 (15) 23

A wide variety of additional alternating constructs have been preparedand screening in various assays is ongoing. Some representativeconstructs that have been made are shown below:

SEQ ID NO/ ISIS NO ANTISENSE SEQUENCES 5′-3′  36/335197 5′-P-T T T G T CT C T G G T C C T T A C T T-OH (AS, PS)  37/335198 5′-P-T T T G T C T CT G G T C C T T A C T T-OH (AS, PS)  38/335201 5′-P-T T T G T C T C T GG T C C T T A C T T-OH (AS, PO)  39/335202 5′-P-T T T G T C T C T G G TC C T T A C T T-OH (AS, PO)  40/335215 5′-P-U T U G U C U C U G G T C CU T A C U T-OH (AS, PS) 413/335216 5′-P-T U T G T C T C T G G U C C T UA C T U-OH (AS, PS)  42/335219 5′-P-U T U G U C U C U G G T C C U T A CU T-OH (AS, PO)  43/335220 5′-P-T U T G T C T C T G G U C C T U A C TU-OH (AS, PO)  44/xxxxx 5′-P-A A G U A A G G A C C A G A G A C A A A-3′(S, PO)  45/xxxxx 5′-P-A A G U A A G G A C C A G A G A C A A A-3′(S, PO)

For the above sequences, underlined is 2′-O-methoxyethyl, for theantisense strands (AS) the bold is 2′-H, for the sense strands (S) thebold is 2′-OH, PS indicates full phosphorothioate, PO indicates fullphosphodiester, 5′-P— is a 5′-phosphate group and all C nucleosides are5′-methyl C′s.

Each of the antisense strands were duplexed with each of the sensestrands to give 16 different siRNA constructs.

46/335211 5′-P-U T U G U C U C U G G T C C U T A C U T-OH (PS) 47/3352125′-P-T U T G T C T C T G G U C C T U A C T U-OH (PS) 48/335213 5′-P-U TU G U C U C U G G T C C U T A C U T-OH (PO) 49/335214 5′-P-T U T G T C TC T G G U C C T U A C T U-OH (PO) 44/xxxxx 5′-P-A A G U A A G G A C C AG A G A C A A A-3′ (S, PO) 45/xxxxx 5′-P-A A G U A A G G A C C A G A G AC A A A-3′ (S, PO)

For the above sequences, underlined is 2′-O-methoxyethyl, for theantisense and the sense strands the bold is 2′-OH, PS indicates fullphosphorothioate, PO indicates full phosphodiester, 5′-P— is a5′-phosphate group and all C nucleosides are 5′-methyl C′s.

Each of the antisense strands were duplexed with each of the sensestrands to give 8 different siRNA constructs.

50/335217 5′-P-U U U G U C U C U G G U C C U U A C U U-OH (PS) 50/3352185′-P-U U U G U C U C U G G U C C U U A C U U-OH (PS) 51/335221 5′-P-U UU G U C U C U G G U C C U U A C U U-OH (PO) 51/335222 5′-P-U U U G U C UC U G G U C C U U A C U U-OH (PO) 36/335199 5′-P-T T T G T C T C T G G TC C T T A C T T-OH (PS) 37/335200 5′-P-T T T G T C T C T G G T C C T T AC T T-OH (PS) 38/335203 5′-P-T T T G T C T C T G G T C C T T A C TT-OH (PO) 39/335204 5′-P-T T T G T C T C T G G T C C T T A C T T-OH (PO)44/xxxxx 5′-P-A A G U A A G G A C C A G A G A C A A A-3′ (S, PO)45/xxxxx 5′-P-A A G U A A G G A C C A G A G A C A A A-3′ (S, PO)

For the above sequences, underlined is 2′-O-methyl, for the antisensestrands (AS) the bold is 2′-H, for the sense strands (S) the bold is2′-OH, PS indicates full phosphorothioate, PO indicates fullphosphodiester, 5′-P— is a 5′-phosphate group and all C nucleosides are5′-methyl C′s.

Each of the antisense strands were duplexed with each of the sensestrands to give 16 different siRNA constructs.

SEQ ID NO: Sequence (5′-3′) 52 TTTGTCTCTGGTCCTTACTT 23UTUGUCUCUGGTCCUTACUT 20 TUTGTCTCTGGUCCTUACTU 12 UUUGUCUCUGGUCCUUACUU 13AAGUAAGGACCAGAGACAAA.

EXAMPLE 7

Reduction of endogenous PTEN mRNA in HeLa cells by 19- and 20-basepairsiRNA is shown in this example. HeLa cells were transfected with siRNAin the presence of lipofectin and treated for 16 hours prior to lysisand analysis by RT-PCR. Maximum % reduction (Max Red) is the amount ofmRNA reduction compared to untreated control cells at the highestconcentration (150 nM), with IC50 indicating the interpolatedconcentration at which 50% reduction is achieved. The notation “5′-P—”indicates the presence of a 5′-phosphate. Bold nucleosides have 2′-OMesubstituents. Otherwise the nucleosides have a 2′-OH substituent. Theconstructs have phosphodiester linkages unless underlined. Underlinednucleosides have phosphorthioate linkages.

SEQ ID IC50 Max No. siRNA (nM) Red 13 5′-AAG UAA GGA CCA GAG ACA AA-3′ 2.4 83 12 3′-UUC AUU CCU GGU CUC UGU UU-P-5′ 135′-AAG UAA GGA CCA GAG ACA AA-3′  1.7 94 563′-UUC AUU CCU GGU CUC UGU UU-P-5′ 14 5′-P-AAG UAA GGA CCA GAG ACA AA-3′ 2.8 60 10 3′-UUC AUU CCU GGU CUC UGU UU-P-5′ 575′-AAG UAA GGA CCA GAG ACA A-3′  0.55 90 583′-UUC AUU CCU GGU CUC UGU U-5′ 59 5′-AAG UAA GGA CCA GAG ACA A-3′  1.295 60 3′-UUC AUU CCU GGU CUC UGU U-5′ 61 5′-GGG UAA AUA CAU UCU ACA U-3′ 1.7 83 62 3′-CCC AUU UAU GUA AGA UGU A-5′ 635′-GGG UAA AUA CAU UCU ACA U-3′  0.63 92 643′-CCC AUU UAU GUA AGA UGU A-5′ 65 5′-UCA AAU CCA GAG GCU AGC A-3′ 13.671 66 3′-AGU UUA GGU CUC CGA UCG U-5′ 67 5′-UCA AAU CCA GAG GCU AGC A-3′n.d. 20 68 3′-AGU UUA GGU CUC CGA UCG U-5′

EXAMPLE 8

Reduction of endogenous PTEN mRNA in HeLa cells by 20-basepair siRNAcontaining 2′-OMe modifications is shown in this example. HeLa cellswere transfected with siRNA in the presence of lipofectin and treatedfor 16 hours prior to lysis and analysis by RT-PCR. Maximum % reductionis the amount of mRNA reduction compared to untreated control cells atthe highest concentration (150 nM), with IC50 indicating theinterpolated concentration at which 50% reduction is achieved. Thenotation “5′-P—” indicates the presence of a 5′-phosphate. Boldnucleosides have 2′-OMe substituents. Otherwise the nucleosides have a2′-OH substituent. The constructs have phosphodiester linkages unlessunderlined. Underlined nucleosides have phosphorthioate linkages.

SEQ ID IC50 Max No. siRNA (nM) Red 13 5′-AAG UAA GGA CCA GAG ACA AA-3′  1.1 79 12 3′-UUC AUU CCU GGU CUC UGU UU-P-5′ 135′-AAG UAA GGA CCA GAG ACA AA-3′   1.2 71 103′-UUC AUU CCU GGU CUC UGU UU-P-5′ 13 5′-AAG UAA GGA CCA GAG ACA AA-3′ 37.4 48 69 3′-UUC AUU CCU GGU CUC UGU UU -P-5′ 145′-P-AAG UAA GGA CCA GAG ACA AA-3′   2.6 60 103′-UUC AUU CCU GGU CUC UGU UU-P-5′ 14 5′-P-AAG UAA GGA CCA GAG ACA AA-3′ 19.2 47 69 3′-UUC AUU CCU GGU CUC UGU UU -P-5′ 705′-P-AAG UAA GGA CCA GAG ACA AA-3′  21.1 59 103′-UUC AUU CCU GGU CUC UGU UU-P-5′ 70 5′-P-AAG UAA GGA CCA GAG ACA AA-3′ 66.6  4 69 3′-UUC AUU CCU GGU CUC UGU U U-P-5′ 135′-AAG UAA GGA CCA GAG ACA AA-3′ 136 47 713′-UUC AUU CCU GGU CUC UGU UU-P-5′ 13 5′-AAG UAA GGA CCA GAG ACA AA-3′440 31 72 3′- UUC AUU CCU GGU CUC UGU U U-P-5′ 705′-P-AAG UAA GGA CCA GAG ACA AA-3′  14.2 62 713′-UUC AUU CCU GGU CUC UGU UU-P-5′ 70 5′-P-AAG UAA GGA CCA GAG ACA AA-3′ 14.7 57 72 3′- UUC AUU CCU GGU CUC UGU U U-P-5′ 145′-P-AAG UAA GGA CCA GAG ACA AA-3′ 179 36 713′-UUC AUU CCU GGU CUC UGU UU-P-5′ 14 5′-P-AAG UAA GGA CCA GAG ACA AA-3′ 29.5 51 72 3′- UUC AUU CCU GGU CUC UGU U U-P-5′

EXAMPLE 9

Reduction of endogenous PTEN mRNA in HeLa cells by 20-basepair siRNAcontaining 2′-F modifications is shown in this example. HeLa cells weretransfected with siRNA in the presence of lipofectin and treated for 16hours prior to lysis and analysis by RT-PCR. Maximum % reduction is theamount of mRNA reduction compared to untreated control cells at thehighest concentration (150 nM), with IC50 indicating the interpolatedconcentration at which 50% reduction is achieved. The notation “5′-P—”indicates the presence of a 5′-phosphate. Bold nucleosides have 2′-Fsubstituents. Otherwise the nucleosides have a 2′-OH substituent. Theconstructs have phosphodiester linkages unless underlined. Underlinednucleosides have phosphorthioate linkages.

SEQ ID IC50 Max No. siRNA (nM) Red 13 5′-AAG UAA GGA CCA GAG ACA AA-3′ 2.5 83 12 3′-UUC AUU CCU GGU CUC UGU UU-P-5′ 135′-AAG UAA GGA CCA GAG ACA AA-3′  0.77 87 733′-UUC AUU CCU GGU CUC UGU UU-P-5′ 13 5′-AAG UAA GGA CCA GAG ACA AA-3′ 2.6 78 74 3′- UUC AUU CCU GGU CUC UGU U U-P-5′ 755′-P-AAG UAA GGA CCA GAG ACA AA-3′  0.67 86 733′-UUC AUU CCU GGU CUC UGU UU-P-5′ 75 5′-AAG UAA GGA CCA GAG ACA AA-3′ 4.7 76 74 3′- UUC AUU CCU GGU CUC UGU U U-P-5′ 765′-P-AAG UAA GGA CCA GAG ACA AA-3′  0.71 86 733′-UUC AUU CCU GGU CUC UGU UU-P-5′ 76 5′-P-AAG UAA GGA CCA GAG ACA AA-3′ 2.8 77 74 3′- UUC AUU CCU GGU CUC UGU U U-P-5′ 135′-AAG UAA GGA CCA GAG ACA AA-3′  1.5 76 773′-UUC AUU CCU GGU CUC UGU UU-P-5′ 13 5′-AAG UAA GGA CCA GAG ACA AA-3′22.9 77 78 3′-UUC AUU CCU GGU CUC UGU UU -P-5′ 765′-P-AAG UAA GGA CCA GAG ACA AA-3′  6.1 71 773′-UUC AUU CCU GGU CUC UGU UU-P-5′ 76 5′-P-AAG UAA GGA CCA GAG ACA AA-3′33.3 57 78 3′-UUC AUU CCU GGU CUC UGU UU -P-5′ 755′-P-AAG UAA GGA CCA GAG ACA AA-3′  5.7 75 773′-UUC AUU CCU GGU CUC UGU UU-P-5′ 75 5′-P-AAG UAA GGA CCA GAG ACA AA-3′54.7 54 78 3′-UUC AUU CCU GGU CUC UGU UU -P-5′

EXAMPLE 10

Reduction of endogenous PTEN mRNA in HeLa cells by 20-basepair siRNAcontaining 2′-F and 2′-deoxy (2′-H) modifications is shown in thisexample. HeLa cells were transfected with siRNA in the presence oflipofectin and treated for 16 hours prior to lysis and analysis byRT-PCR. Maximum % reduction is the amount of mRNA reduction compared tountreated control cells at the highest concentration (150 nM), with IC50indicating the interpolated concentration at which 50% reduction isachieved. The notation “5′-P—” indicates the presence of a 5′-phosphate.Bold nucleosides have 2′-F substituents. Nucleosides with a “d”subscript have a deoxy sugar. Otherwise the nucleosides have a 2′-OHsubstituent. The constructs have phosphodiester linkages unlessunderlined. Underlined nucleosides have phosphorthioate linkages.

SEQ IC50 Max ID No. siRNA (nM) Red 13 5′-AAG UAA GGA CCA GAG ACA AA-3′  2.6 76 12 3′-UUC AUU CCU GGU CUC UGU UU-P-5′ 135′-AAG UAA GGA CCA GAG ACA AA-3′  11.7 60 79 3′-UT_(d) C A_(d)UT_(d) CC_(d) U G_(d) GT_(d) CT_(d) C T_(d) GT_(d) UT_(d)-P-5′ 135′-AAG UAA GGA CCA GAG ACA AA-3′  76.7 54 80 3′- UT_(d) C A_(d)UT_(d) CC_(d) U G_(d) GT_(d) CT_(d) C T_(d) GT_(d) UT_(d) -P-5′ 815′-A_(d) AG_(d) UA_(d) A G_(d) GA_(d) CC_(d) A G_(d) AG_(d) AC_(d)A A_(d) A-3′ 100 49 79 3′-UT_(d) C A_(d) UT_(d) CC_(d) U G_(d)GT_(d) CT_(d) C T_(d) GT_(d) UT_(d)-P-5′ 81 5′-A_(d) AG_(d) UA_(d)A G_(d) GA_(d) CC_(d) A G_(d) AG_(d) AC_(d) A A_(d) A-3′  50.7 66 80 3′-UT_(d) C A_(d) UT_(d) CC_(d) U G_(d) GT_(d) CT_(d) C T_(d) GT_(d) UT_(d)-P-5′ 82 5′-AA_(d) G T_(d) AA_(d) GG_(d) A C_(d) CA_(d) GA_(d) G A_(d)CA_(d) AA_(d)-3′ 122 48 79 3′-UT_(d) C A_(d) UT_(d) CC_(d) U G_(d)GT_(d) CT_(d) C T_(d) GT_(d) UT_(d)-P-5′ 82 5′-AA_(d) G T_(d)AA_(d) GG_(d) A C_(d) CA_(d) GA_(d) G A_(d) CA_(d) AA_(d)-3′  55.7 57 803′- UT_(d) C A_(d) UT_(d) CC_(d) U G_(d) GT_(d) CT_(d) C T_(d)GT_(d) UT_(d) -P-5′ 13 5′-AAG UAA GGA CCA GAG ACA AA-3′ n.d. 35 833′-TU_(d) C A_(d) TU_(d) CC_(d) T G_(d) GU_(d) CU_(d) C U_(d)GU_(d) TU_(d)-P-5′ 13 5′-AAG UAA GGA CCA GAG ACA AA-3′  66.8 48 84 3′-TU_(d) C A_(d) TU_(d) CC_(d) T G_(d) GU_(d) CU_(d) C U_(d) GU_(d) TU_(d)-P-5′ 82 5′-AA_(d) G T_(d) AA_(d) GG_(d) A C_(d) CA_(d) GA_(d) G A_(d)CA_(d) AA_(d)-3′ n.d. 22 83 3′-TU_(d) C A_(d) TU_(d) CC_(d) T G_(d)GU_(d) CU_(d) C U_(d) GU_(d) TU_(d)-P-5′ 82 5′-AA_(d) G T_(d)AA_(d) GG_(d) A C_(d) CA_(d) GA_(d) G A_(d) CA_(d) AA_(d)-3′ 145 66 843′- TU_(d) C A_(d) TU_(d) CC_(d) T G_(d) GU_(d) CU_(d) C U_(d)GU_(d) TU_(d) -P-5′ 81 5′-A_(d) AG_(d) UA_(d) A G_(d) GA_(d) CC_(d)A G_(d) AG_(d) AC_(d) A A_(d) A-3′ n.d.  9 83 3′-TU_(d) C A_(d)TU_(d) CC_(d) T G_(d) GU_(d) CU_(d) C U_(d) GU_(d) TU_(d)-P-5′ 815′-A_(d) AG_(d) UA_(d) A G_(d) GA_(d) CC_(d) A G_(d) AG_(d) AC_(d)A A_(d) A-3′ 158 58 84 3′- TU_(d) C A_(d) TU_(d) CC_(d) T G_(d)GU_(d) CU_(d) C U_(d) GU_(d) TU_(d) -P-5′

EXAMPLE 11

Reduction of endogenous PTEN mRNA in HeLa cells by 20-basepair siRNAcontaining 2′-F and 2′-OMe modifications is shown in this example. HeLacells were transfected with siRNA in the presence of lipofectin andtreated for 16 hours prior to lysis and analysis by RT-PCR. Maximum %reduction is the amount of mRNA reduction compared to untreated controlcells at the highest concentration (150 nM), with IC50 indicating theinterpolated concentration at which 50% reduction is achieved. Thenotation “5′-P—” indicates the presence of a 5′-phosphate. Boldnucleosides have 2′-F substituents. Nucleosides with a “m” subscripthave 2′-OMe substituents. Otherwise the nucleosides have a 2′-OHsubstituent. The constructs have phosphodiester linkages unlessunderlined. Underlined nucleosides have phosphorthioate linkages.

SEQ IC50 Max ID No. siRNA (nM) Red  13 5′-AAG UAA GGA CCA GAG ACA AA-3′  1.5  86  12 3′-UUC AUU CCU GGU CUC UGU UU-P-5′  135′-AAG UAA GGA CCA GAG ACA AA-3′   0.18 87  85 3′- UU_(m) C A_(m)UU_(m) CC_(m) U G_(m) GU_(m) CU_(m) C U_(m) GU_(m) UU_(m) -P-5′  135′-AAG UAA GGA CCA GAG ACA AA-3′  23.4  66  86 3′-UU_(m) C A_(m)UU_(m) CC_(m) U G_(m) GU_(m) CU_(m) C U_(m) GU_(m) UU_(m)-P-5′ 1325′-A_(m) AG_(m) UA_(m) A G_(m) GA_(m) CC_(m) A G_(m) AG_(m) AC_(m)A A_(m) A-3′   3.8  80  86 3′-UU_(m) C A_(m) UU_(m) CC_(m) U G_(m)GU_(m) CU_(m) C U_(m) GU_(m) UU_(m)-P-5′ 132 5′-A_(m) AG_(m) UA_(m)A G_(m) GA_(m) CC_(m) A G_(m) AG_(m) AC_(m) A A_(m) A-3′  92    59  853′- UU_(m) C A_(m) UU_(m) CC_(m) U G_(m) GU_(m) CU_(m) C U_(m)GU_(m) UU_(m) -P-5′ 133 5′-AA_(m) G U_(m) AA_(m) GG_(m) A C_(m)CA_(m) GA_(m) G A_(m) CA_(m) AA_(m)-3′ 192    48  87 3′-UU_(m) C A_(m)UU_(m) CC_(m) U G_(m) GU_(m) CU_(m) C U_(m) GU_(m) UU_(m)-P-5′ 1335′-AA_(m) G U_(m) AA_(m) GG_(m) A C_(m) CA_(m) GA_(m) G A_(m)CA_(m) AA_(m)-3′   3.4  84  85 3′- UU_(m) C A_(m) UU_(m) CC_(m) U G_(m)GU_(m) CU_(m) C U_(m) GU_(m) UU_(m) -P-5′  135′-AAG UAA GGA CCA GAG ACA AA-3′   3.8  70 134 3′-U_(m) UC_(m) AU_(m)U C_(m) CU_(m) GG_(m) U C_(m) UC_(m) UG_(m) U U_(m) U-P-5′  135′-AAG UAA GGA CCA GAG ACA AA-3′  53.2  52 135 3′-U_(m) UC_(m) AU_(m)U C_(m) CU_(m) GG_(m) U C_(m) UC_(m) UG_(m) U U_(m) U -P-5′ 1335′-AA_(m) G U_(m) AA_(m) GG_(m) A C_(m) CA_(m) GA_(m) G A_(m)CA_(m) AA_(m)-3′   3.5  82 134 3′-U_(m) UC_(m) AU_(m) U C_(m)CU_(m) GG_(m) U C_(m) UC_(m) UG_(m) U U_(m) U-P-5′ 133 5′-AA_(m) G U_(m)AA_(m) GG_(m) A C_(m) CA_(m) GA_(m) G A_(m) CA_(m) AA_(m)-3′ n.d. 13 1353′-U_(m) UC_(m) AU_(m) U C_(m) CU_(m) GG_(m) U C_(m) UC_(m) UG_(m)U U_(m) U -P-5′ 132 5′-A_(m) AG_(m) UA_(m) A G_(m) GA_(m) CC_(m) A G_(m)AG_(m) AC_(m) A A_(m) A-3′ n.d. 27 134 3′-U_(m) UC_(m) AU_(m) U C_(m)CU_(m) GG_(m) U C_(m) UC_(m) UG_(m) U U_(m) U-P-5′ 132 5′-A_(m)AG_(m) UA_(m) A G_(m) GA_(m) CC_(m) A G_(m) AG_(m) AC_(m) A A_(m) A-3′n.d. 32 132 3′-U_(m) UC_(m) AU_(m) U C_(m) CU_(m) GG_(m) U C_(m)UC_(m) UG_(m) U U_(m) U -P-5′

EXAMPLE12

Reduction of endogenous PTEN mRNA in HeLa cells by 19-basepair siRNAscontaining 2′-F and 2′-OMe modifications is shown in this example. HeLacells were transfected with siRNA in the presence of lipofectin andtreated for 16 hours prior to lysis and analysis by RT-PCR. Maximum %reduction is the amount of mRNA reduction compared to untreated controlcells at the highest concentration (150 nM), with IC50 indicating theinterpolated concentration at which 50% reduction is achieved. Thenotation “5′-P—” indicates the presence of a 5′-phosphate. Boldnucleosides have 2′-F substituents. Nucleosides with a “m” subscripthave 2′-OMe substituents. Otherwise the nucleosides have a 2′-OHsubstituent. The constructs have phosphodiester linkages unlessunderlined. Underlined nucleosides have phosphorthioate linkages.

SEQ IC50 Max ID No. siRNA (nM) Red 57 5′-AAG UAA GGA CCA GAG ACA AA-3′0.55 74 58 3′-UUC AUU CCU GGU CUC UGU UU-P-5′ 575′-AAG UAA GGA CCA GAG ACA AA-3′ 0.66 74 88 3′-U_(m) UC_(m) AU_(m)U C_(m) CU_(m) GG_(m) U C_(m) UC_(m) UG_(m) U U_(m) U-P-5′ 89 5′-AA_(m)G U_(m) AA_(m) GG_(m) A C_(m) CA_(m) GA_(m) G A_(m) CA_(m) AA_(m)-3′0.38 81 88 3′-U_(m) UC_(m) AU_(m) U C_(m) CU_(m) GG_(m) U C_(m)UC_(m) UG_(m) U U_(m) U-P-5′ 61 5′-GGG UAA AUA CAU UCU ACA U-3′ 7.4  5862 3′-CCC AUU UAU GUA AGA UGU A-5′ 61 5′-GGG UAA AUA CAU UCU ACA U-3′0.29 80 90 3′-C_(m) CC_(m) AU_(m) U U_(m) AU_(m) GU_(m) A A_(m)GA_(m) UG_(m) U A_(m)-5′ 91 5′-GG_(m) G U_(m) AA_(m) AU_(m) A C_(m)AU_(m) UC_(m) U A_(m) CA_(m) U-3′ 0.03 88 90 3′-C_(m) CC_(m) AU_(m)U U_(m) AU_(m) GU_(m) A A_(m) GA_(m) UG_(m) U A_(m)-5′

EXAMPLE13

Additional Alternating Sequences

The following sequences were prepared. Subscripts denote structuralmodifications. These codes are consistent with IUPAC rules onbiochemical nomenclature. As used herein, any first lower case letterfollowing the base code represents a sugar feature. In particular, “m”is 2′-O-methyl; “r” is ribo; “e” is 2′-O-methoxyethyl (MOE); “f” is2′-deoxy-2′-fluoro; and “s” is 4′-thioribose. Any second lower caseletter after the base code represents a linkage feature. In particular,“s” is a phosphorothioate linkage; and “o” is a phosphodiester linkage.For example Ums is has a uracil base, a 2′-O-methoxy group on the sugarand a phosphorthioate linkage to the sugar of the nucleoside thatfollows.

SEQ ID NO/ISIS NO SEQUENCES (5′-3′) Alternating 2′-OCH₃/2′-OH full P =S as/s RNA   136 (as)/335454UmsUrsUmsGrsUmsCrsUmsCrsUmsGrsGmsUrsCmsCrsUmsUrsAmsCrsUmsU    13 (s)/308746 AAGUAAGGACCAGAGACAAAAlternating 2′-OCH₃/2′-OH as/s RNA    10 (as)/335456UmoUUmoGUmoCUmoCUmoGGmoUCmoCUmoUAmoCUmoU     13 (s)/308746AAGUAAGGACCAGAGACAAA   137 (as)/344217UUfoUGfoUCfoUCfoUGfoGUfoCCfoUUfoACfoUUf     13 (s)/308746AAGUAAGGACCAGAGACAAA    92 (as)/352507UmoUUmoGAmoAAmoAUmoGUmoUGmoAUmoCUmoCCm     93 (s)/343868GGAGAUCAACAUUUUCAAA Alternating 2′-OCH₃/2′-OH as/s 2′-OCH₃/2′-OH   10 (as)/335456 UmoUUmoGUmoCUmoCUmoGGmoUCmoCUmoUAmoCUmoU    14 (s)/335452 AmoAGmoUAmoAGmoGAmoCCmoAGmoAGmoACmoAAmoA   94 (as)/341396 UmoUGmoUCmoUCmoUGmoGUmoCCmoUUmoACmoUUm    59 (s)/341406 AAmoGUmoAAmoGGmoACmoCAmoGAmoGAmoCAmoA   95 (as)/345847 UmoCUmoUAmoUCmoACmoCUmoUUmoAGmoCUmoCUm    96 (s)/345849 AGmoAGmoCUmoAAmoAGmoGUmoGAmoUAmoAGmoA   92 (as)/352507 UmoUUmoGAmoAAmoAUmoGUmoUGmoAUmoCUmoCCm    97 (s)/352511 GGmoAGmoAUmoCAmoACmoAUmoUUmoUCmoAAmoA   92 (as)/352507 UmoUUmoGAmoAAmoAUmoGUmoUGmoAUmoCUmoCCm    98 (s)/352512GmoGmoAmoGmoAmoUmoCmoAmoAmoCmoAmoUmoUmoUmoUmoCmoAmoAmoAm   92 (as)/352507 UmoUUmoGAmoAAmoAUmoGUmoUGmoAUmoCUmoCCm     99(s)/352513 GGmoAmoGmoAmoUmoCmoAmoAmoCmoAmoUmoUmoUmoUmoCmoAmoAmoAAlternating 2′-F/2′-OH as/s 2′-F/2′-OH   138 (as)/344217UUfoUGfoUCfoUCfoUGfoGUfoCCfoUUfoACfoUUf    139 (s)/344221AfoAGfoUAfoAGfoGAfoCCfoAGfoAGfoACfoAAfoA   138 (as)/344217UUfoUGfoUCfoUCfoUGfoGUfoCCfoUUfoACfoUUf    140 (s)/344222AAfoGUfoAAfoGGfoACfoCAfoGAfoGAfoCAfoAAf Alternating 2′-H (d =deoxy)/2′-F as/s RNA    17 (as)/339923TdoUfoTdoGfoTdoCfoTdoCfoTdoGfoGdoUfomCdoCfoTdoUfoAdoCfoTdoUf    13 (s)/308746 AAGUAAGGACCAGAGACAAA Alternating 2′-OCH₃/2′-F as/s RNA  141 (as)/340569UmoUfoUmoGfoUmoCfoUmoCfoUmoGfoGmoUfoCmoCfoUmoUfoAmoCfoUmoUf    13 (s)/308746 AAGUAAGGACCAGAGACAAA   142 (as)/340571UfoUmoUfoGmoUfoCmoUfoCmoUfoGmoGfoUmoCfoCmoUfoUmoAfoCmoUfoUm    13 (s)/308746 AAGUAAGGACCAGAGACAAA   100 (as)/352820UmoUfoGmoUfoCmoUfoCmoUfoGmoGfoUmoCfoCmoUfoUmoAfoCmoUfoUm    57 (s)/341401 AAGUAAGGACCAGAGACAAAlternating 2′-OCH₃/2′-F as/s 2′-OCH₃/2′-F   141 (as)/340569UmoUfoUmoGfoUmoCfoUmoCfoUmoGfoGmoUfoCmoCfoUmoUfoAmoCfoUmoUf   143 (s)/340574AmoAfoGmoUfoAmoAfoGmoGfoAmoCfoCmoAfoGmoAfoGmoAfoCmoAfoAmoAf  144 (as)/340571UfoUmoUfoGmoUfoCmoUfoCmoUfoGmoGfoUmoCfoCmoUfoUmoAfoCmoUfoUm   145 (s)/340573AfoAmoGfoUmoAfoAmoGfoGmoAfoCmoCfoAmoGfoAmoGfoAmoCfoAmoAfoAm  100 (as)/352820UmoUfoGmoUfoCmoUfoCmoUfoGmoGfoUmoCfoCmoUfoUmoAfoCmoUfoUm   146 (s)/352821AfoAmoGfoUmoAfoAmoGfoGmoAfoCmoCfoAmoGfoAmoGfoAmoCfoAmoAf  101 (as)/351827 UmoGfoUmoCfoAmoUfoAmoUfoUmoCfoCmoUfoGmoGfoAmo   102 (s)/351828AfoGmoGfoAmoUfoCmoCfoAmoGfoGmoAfoAmoUfoAmoUfoGmoAfoCmoAf  103 (as)/351829UmoCfoCmoUfoGmoGfoAmoUfoCmoCfoUmoUfoCmoAfoCmoCfoAmoAfoUm   104 (s)/351830AfoUmoUfoGmoGfoUmoGfoAmoAfoGmoGfoAmoUfoCmoCfoAmoGfoGmoAf  105 (as)/351831UmoCfoUmoUfoAmoUfoCmoAfoCmoCfoUmoUfoUmoAfoGmoCfoUmoCfoUm   106 (s)/351832AfoGmoAfoGmoCfoUmoAfoAmoAfoGmoGfoUmoGfoAmoUfoAmoAfoGmoAf  107 (as)/351833AmoUfoAmoCfoUmoCfoAmoGfoAmoAfoGmoGfoUmoGfoUmoCfoUmoUfoCm   108 (s)/351834GfoAmoAfoGmoAfoCmoAfoCmoCfoUmoUfoCmoUfoGmoAfoGmoUfoAmoUf  109 (as)/355713UmoUfoUmoGfoAmoAfoAmoAfoUmoGfoUmoUfoGmoAfoUmoCfoUmoCfoCm   110 (s)/355714GfoGmoAfoGmoAfoUmoCfoAmoAfoCmoAfoUmoUfoUmoUfoCmoAfoAmoAfAlternating 2′-OCH₃/2′-F full P = S as/s 2′-OCH₃/2′-F   147 (as)/340570UmsUfsUmsGfsUmsCfsUmsCfsUmsGfsGmsUfsCmsCfsUmsUfsAmsCfsUmsUf   145 (s)/340573AfoAmoGfoUmoAfoAmoGfoGmoAfoCmoCfoAmoGfoAmoGfoAmoCfoAmoAfoAmAlternating 2′-F/2′-OH as/s RNA   148 (as)/344219UfoUUfoGUfoCUfoCUfoGGfoUCfoCUfoUAfoCUfoU     13 (s)/308746AAGUAAGGACCAGAGACAAAAlternating 2′-OCH₃/2′-OH as/s alternating 2′-MOE/2′-OH   92 (as)/352507 UmoUUmoGAmoAAmoAUmoGUmoUGmoAUmoCUmoCCm   111 (s)/352514 GGeoAGeoAUeoCAeoACeoAUeoUUeoUCeoAAeoA Full P =S RNA as/s alternating 2′-MOE/2′-OH   149 (as)/346280UrsUrsUrsGrsArsArsArsArsUrsGrsUrsUrsGrsArsUrsCrsUrsCrsCrsU   111 (s)/352514 GGeoAGeoAUeoCAeoACeoAUeoUUeoUCeoAAeoA Full P =S as/s alternating 2′-OH/2′-OCH₃ alternating P = O/P = S  112 (as)/346280UrsUrsUrsGrsArsArsArsArsUrsGrsUrsUrsGrsArsUrsCrsUrsCrsCrsU    97 (s)/352511 GGmoAGmoAUmoCAmoACmoAUmoUUmoUCmoAAmoAAlternating 2′-OCH₃/2′-OH as/s full P = S RNA    92 (as)/352507UmoUUmoGAmoAAmoAUmoGUmoUGmoAUmoCUmoCCm    113 (s)/346287GrsGrsArsGrsArsUrsCrsArsArsCrsArsUrsUrsUrsUrsCrsArsArsAGapmers having alternating wing motifs in one or both strands2′-OCH₃/2′-OH wing/RNA gap/2′-OCH₃/2′-OH wing as/s full alternating 2′-OCH₃/2′-OH 114 (as-P)/353563UmoUGmoUCmoUCUGGUCCUUmoACmoUUm     59 (s)/341406AAmoGUmoAAmoGGmoACmoCAmoGAmoGAmoCAmoA 115 (as-P)/353565UmoGCmoUAmoGCCUCUGGAUmoUUmoGAm    116 (s)/341405UCmoAAmoAUmoCCmoAGmoAGmoGCmoUAmoGCmoA2′-OCH₃/2′-OH wing/RNA gap/2′-OCH₃/2′-OH wing both as and s114 (as-P)/353563 UmoUGmoUCmoUCUGGUCCUUmoACmoUUm    117 (s)/353564AAmoGUmoAAGGACCAGAGAmoCAmoA 115 (as-P)/353565UmoGCmoUAmoGCCUCUGGAUmoUUmoGAm    118 (s)/353566UCmoAAmoAUCCAGAGGCUAmoGCmoA

EXAMPLE 14

Assays of Example 13 Constructs

The constructs of example 13 were tested in accordance with the assaysdescribed herein. Cell line 20 is HeLa. Cell line 160 is U-87 MG. Cellline 243 is MH-S. Cells are available from commercial sources. Forexample, HeLa cells can be obtained from American Type CultureCollection, Manassas Va. Culture methods used for HeLa cells areavailable from the ATCC and may be found, for example, athttp://www.atcc.org. For cells grown in 96-well plates, wells werewashed once with 200 μL OPTI-MEM-1 reduced-serum medium (Gibco BRL) andthen treated with 130 μL of OPTI-MEM-1 containing 12 μg/mL LIPOFECTIN™(Gibco BRL) and the dsRNA at the desired concentration. After 5 hours oftreatment, the medium was replaced with fresh medium. Cells wereharvested 16 hours after dsRNA treatment, at which time RNA was isolatedand target reduction measured by RT-PCR as described in previousexamples.

Construct Assay/Species Target Cell Line IC50 (nM) 335454:308746 DoseResponse/Human PTEN 20 3.31 335456:308746 Dose Response/Human PTEN 200.449 344217:308746 Dose Response/Human PTEN 20 0.597 352507:343868 DoseResponse/Human Survivin 20 1.0171 335456:335452 Dose Response/Human PTEN20 0.248 341396:341406 Dose Response/Human PTEN 20 1.0316 345847:345849RTPCR EIF4E MH-S/Mouse eIF4E 243 0.27303 352507:352511 DoseResponse/Human Survivin 20 0.23734 352507:352511 Dose Response/HumanSurvivin 160 0.37 352507:352511 Dose Response/Human Survivin 20 0.47352507:352512 Dose Response/Human Survivin 20 0.039396 352507:352512Dose Response/Human Survivin 20 0.6 352507:352513 Dose Response/HumanSurvivin 20 0.34906 344217:344221 Dose Response/Human PTEN 20 0.674344217:344222 Dose Response/Human PTEN 20 0.345 339923:308746 DoseResponse/Human PTEN 20 0.466 340569:308746 Dose Response/Human PTEN 200.263 340571:308746 Dose Response/Human PTEN 20 3.32 352820:341401 DoseResponse/Human PTEN 20 1.0348 340569:340574 Dose Response/Human PTEN 200.496 340571:340573 Dose Response/Human PTEN 20 1.36 352820:352821 DoseResponse/Human PTEN 20 0.28988 351827:351828 RTPCR EIF4E MH-S/MouseeIF4E 243 0.054034 351829:351830 RTPCR EIF4E MH-S/Mouse eIF4E 2430.50058 351831:351832 RTPCR EIF4E MH-S/Mouse eIF4E 243 0.051497351833:351834 RTPCR EIF4E MH-S/Mouse eIF4E 243 0.092224 355713:355714Dose Response/Human Survivin 20 0.064756 355713:355714 DoseResponse/Human Survivin 20 0.064756 355713:355714 Dose Response/HumanSurvivin 20 078878 355713:355714 Dose Response/Human Survivin 160 0.107355713:355714 Dose Response/Human Survivin 20 0.151 340570:340573 DoseResponse/Human PTEN 20 1.83 344219:308746 Dose Response/Human PTEN 200.886 352507:352514 Dose Response/Human Survivin 20 0.21038352507:352514 Dose Response/Human Survivin 160 0.538 352507:352514 DoseResponse/Human Survivin 20 0.547 346280:352514 Dose Response/HumanSurvivin 20 1.0094 346280:352511 Dose Response/Human Survivin 20 1.4662352507:346287 Dose Response/Human Survivin 20 0.42207 353563:341406 DoseResponse/Human PTEN 20 0.78421 353563:341406 Dose Response/Human PTEN 200.88581 353565:341405 Dose Response/Human PTEN 20 17.275 353563:353564Dose Response/Human PTEN 20 0.27194 353563:353564 Dose Response/HumanPTEN 20 5.2523 353565:353566 Dose Response/Human PTEN 20 5.7721

EXAMPLE 15

Synthesis of Nucleoside Phosphoramidites

The following compounds, including amidites and their intermediates wereprepared as described in U.S. Pat. No. 6,426,220 and published PCT WO02/36743; 5′-O-Dimethoxytrityl-thymidine intermediate for 5-methyl dCamidite, 5′-O-Dimethoxytrityl-2′-deoxy-5-methylcytidine intermediate for5-methyl-dC amidite,5′-O-Dimethoxytrityl-2′-deoxy-N4-benzoyl-5-methylcytidine penultimateintermediate for 5-methyl dC amidite,[5′-O-(4,4′-Dimethoxytriphenylmethyl)-2′-deoxy-N⁴-benzoyl-5-methylcytidin-3′-O-yl]-2-cyanoethyl-N,N-diisopropylphosphoramidite(5-methyl dC amidite), 2′-Fluorodeoxyadenosine, 2′-Fluorodeoxyguanosine,2′-Fluorouridine, 2′-Fluorodeoxycytidine, 2′-O-(2-Methoxyethyl) modifiedamidites, 2′-O-(2-methoxyethyl)-5-methyluridine intermediate,5′-O-DMT-2′-O-(2-methoxyethyl)-5-methyluridine penultimate intermediate,[5′-O-(4,4′-Dimethoxytriphenylmethyl)-2′-O-(2-methoxyethyl)-5-methyluridin-3′-O-yl]-2-cyanoethyl-N,N-diisopropylphosphoramidite(MOE T amidite),5′-O-Dimethoxytrityl-2′-O-(2-methoxyethyl)-5-methylcytidineintermediate,5′-O-dimethoxytrityl-2′-O-(2-methoxyethyl)-N⁴-benzoyl-5-methyl-cytidinepenultimate intermediate,[5′-O-(4,4′-Dimethoxytriphenylmethyl)-2′-O-(2-methoxyethyl)-N⁴-benzoyl-5-methylcytidin-3′-O-yl]-2-cyanoethyl-N,N-diisopropylphosphoramidite(MOE 5-Me-C amidite),[5′-O-(4,4′-Dimethoxytriphenylmethyl)-2′-O-(2-methoxyethyl)-N⁶-benzoyladenosin-3′-O-yl]-2-cyanoethyl-N,N-diisopropylphosphoramidite(MOE A amdite),[5′-O-(4,4′-Dimethoxytriphenylmethyl)-2′-O-(2-methoxyethyl)-N⁴-isobutyrylguanosin-3′-O-yl]-2-cyanoethyl-N,N-diisopropylphosphoramidite(MOE G amidite), 2′-O-(Aminooxyethyl) nucleoside amidites and2′-O-(dimethylaminooxyethyl) nucleoside amidites,2′-(Dimethylaminooxyethoxy) nucleoside amidites,5′-O-tert-Butyldiphenylsilyl-O²-2′-anhydro-5-methyluridine,5′-O-tert-Butyldiphenylsilyl-2′-O-(2-hydroxyethyl)-5-methyluridine,2′-O-([2-phthalimidoxy)ethyl]-5′-t-butyldiphenylsilyl-5-methyluridine,5′-O-tert-butyldiphenylsilyl-2′-O-[(2-formadoximinooxy)ethyl]-5-methyluridine,5′-O-tert-Butyldiphenylsilyl-2′-O-[N,Ndimethylaminooxyethyl]-5-methyluridine,2′-O-(dimethylaminooxyethyl)-5-methyluridine,5′-O-DMT-2′-O-(dimethylaminooxyethyl)-5-methyluridine,5′-O-DMT-2′-O-(2-N,N-dimethylaminooxyethyl)-5-methyluridine-3′-[(2-cyanoethyl)-N,N-diisopropylphosphoramidite],2′-(Aminooxyethoxy) nucleoside amidites,N2-isobutyryl-6-0-diphenylcarbamoyl-2′-O-(2-ethylacetyl)-5′-O-(4,4′-dimethoxytrityl)guanosine-3′-[(2-cyanoethyl)-N,N-diisopropylphosphoramidite],2′-dimethylaminoethoxyethoxy (2′-DMAEOE) nucleoside amidites,2′-O-[2(2-N,N-dimethylaminoethoxy)ethyl]-5-methyl uridine,5′-O-dimethoxytrityl-2′-O-[2(2-N,N-dimethylaminoethoxy)-ethyl)]-5-methyluridine and 5′-O-Dimethoxytrityl-2′-O-[2(2-N,N-dimethylaminoethoxy)-ethyl)]-5-methyluridine-3′-O-(cyanoethyl-N,N-diisopropyl)phosphoramidite.

EXAMPLE 16

Oligonucleotide and Oligonucleoside Synthesis

The oligonucleotides used in accordance with this invention may beconveniently and routinely made through the well-known technique ofsolid phase synthesis. Equipment for such synthesis is sold by severalvendors including, for example, Applied Biosystems (Foster City,Calif.). Any other means for such synthesis known in the art mayadditionally or alternatively be employed. It is well known to usesimilar techniques to prepare oligonucleotides such as thephosphorothioates and alkylated derivatives.

Oligonucleotides: Unsubstituted and substituted phosphodiester (P═O)oligonucleotides are synthesized on an automated DNA synthesizer(Applied Biosystems model 394) using standard phosphoramidite chemistrywith oxidation by iodine.

Phosphorothioates (P═S) are synthesized similar to phosphodiesteroligonucleotides with the following exceptions: thiation was effected byutilizing a 10% w/v solution of 3,H-1,2-benzodithiole-3-one 1,1-dioxidein acetonitrile for the oxidation of the phosphite linkages. Thethiation reaction step time was increased to 180 sec and preceded by thenormal capping step. After cleavage from the CPG column and deblockingin concentrated ammonium hydroxide at 55° C. (12-16 hr), theoligonucleotides were recovered by precipitating with >3 volumes ofethanol from a 1 M NH₄OAc solution. Phosphinate oligonucleotides areprepared as described in U.S. Pat. No. 5,508,270, herein incorporated byreference.

Alkyl phosphonate oligonucleotides are prepared as described in U.S.Pat. No. 4,469,863, herein incorporated by reference.

3′-Deoxy-3′-methylene phosphonate oligonucleotides are prepared asdescribed in U.S. Pat. Nos. 5,610,289 or 5,625,050, herein incorporatedby reference.

Phosphoramidite oligonucleotides are prepared as described in U.S. Pat.Nos., 5,256,775 or 5,366,878, herein incorporated by reference.

Alkylphosphonothioate oligonucleotides are prepared as described inpublished PCT applications PCT/US94/00902 and PCT/US93/06976 (publishedas WO 94/17093 and WO 94/02499, respectively), herein incorporated byreference.

3′-Deoxy-3′-amino phosphoramidate oligonucleotides are prepared asdescribed in U.S. Pat. No. 5,476,925, herein incorporated by reference.

Phosphotriester oligonucleotides are prepared as described in U.S. Pat.No. 5,023,243, herein incorporated by reference.

Borano phosphate oligonucleotides are prepared as described in U.S. Pat.Nos. 5,130,302 and 5,177,198, both herein incorporated by reference.

Oligonucleosides: Methylenemethylimino linked oligonucleosides, alsoidentified as MMI linked oligonucleosides, methyl enedimethylhydrazolinked oligonucleosides, also identified as MDH linked oligonucleosides,and methylenecarbonylamino linked oligonucleosides, also identified asamide-3 linked oligonucleosides, and methyleneaminocarbonyl linkedoligo-nucleosides, also identified as amide-4 linked oligonucleosides,as well as mixed backbone oligonucleotides having, for instance,alternating MMI and P═O or P═S linkages are prepared as described inU.S. Pat. Nos. 5,378,825, 5,386,023, 5,489,677, 5,602,240 and 5,610,289,all of which are herein incorporated by reference.

Formacetal and thioformacetal linked oligonucleosides are prepared asdescribed in U.S. Pat. Nos. 5,264,562 and 5,264,564, herein incorporatedby reference.

Ethylene oxide linked oligonucleosides are prepared as described in U.S.Pat. No. 5,223,618, herein incorporated by reference.

EXAMPLE 17

RNA Synthesis

In general, RNA synthesis chemistry is based on the selectiveincorporation of various protecting groups at strategic intermediaryreactions. Although one of ordinary skill in the art will understand theuse of protecting groups in organic synthesis, a useful class ofprotecting groups includes silyl ethers. In particular bulky silylethers are used to protect the 5′-hydroxyl in combination with anacid-labile orthoester protecting group on the 2′-hydroxyl. This set ofprotecting groups is then used with standard solid-phase synthesistechnology. It is important to lastly remove the acid labile orthoesterprotecting group after all other synthetic steps. Moreover, the earlyuse of the silyl protecting groups during synthesis ensures facileremoval when desired, without undesired deprotection of 2′ hydroxyl.

Following this procedure for the sequential protection of the5′-hydroxyl in combination with protection of the 2′-hydroxyl byprotecting groups that are differentially removed and are differentiallychemically labile, RNA oligonucleotides were synthesized.

RNA oligonucleotides are synthesized in a stepwise fashion. Eachnucleotide is added sequentially (3′- to 5′-direction) to a solidsupport-bound oligonucleotide. The first nucleoside at the 3′-end of thechain is covalently attached to a solid support. The nucleotideprecursor, a ribonucleoside phosphoramidite, and activator are added,coupling the second base onto the 5′-end of the first nucleoside. Thesupport is washed and any unreacted 5′-hydroxyl groups are capped withacetic anhydride to yield 5′-acetyl moieties. The linkage is thenoxidized to the more stable and ultimately desired P(V) linkage. At theend of the nucleotide addition cycle, the 5′-silyl group is cleaved withfluoride. The cycle is repeated for each subsequent nucleotide.

Following synthesis, the methyl protecting groups on the phosphates arecleaved in 30 minutes utilizing 1 Mdisodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate (S₂Na₂)in DMF. The deprotection solution is washed from the solid support-boundoligonucleotide using water. The support is then treated with 40%methylamine in water for 10 minutes at 55° C. This releases the RNAoligonucleotides into solution, deprotects the exocyclic amines, andmodifies the 2′-groups. The oligonucleotides can be analyzed by anionexchange HPLC at this stage.

The 2′-orthoester groups are the last protecting groups to be removed.The ethylene glycol monoacetate orthoester protecting group developed byDharmacon Research, Inc. (Lafayette, Colo.), is one example of a usefulorthoester protecting group which, has the following importantproperties. It is stable to the conditions of nucleoside phosphoramiditesynthesis and oligonucleotide synthesis. However, after oligonucleotidesynthesis the oligonucleotide is treated with methylamine which not onlycleaves the oligonucleotide from the solid support but also removes theacetyl groups from the orthoesters. The resulting 2-ethyl-hydroxylsubstituents on the orthoester are less electron withdrawing than theacetylated precursor. As a result, the modified orthoester becomes morelabile to acid-catalyzed hydrolysis. Specifically, the rate of cleavageis approximately 10 times faster after the acetyl groups are removed.Therefore, this orthoester possesses sufficient stability in order to becompatible with oligonucleotide synthesis and yet, when subsequentlymodified, permits deprotection to be carried out under relatively mildaqueous conditions compatible with the final RNA oligonucleotideproduct.

Additionally, methods of RNA synthesis are well known in the art(Scaringe, S. A. Ph.D. Thesis, University of Colorado, 1996; Scaringe,S. A., et al., J. Am. Chem. Soc., 1998, 120, 11820-11821; Matteucci, M.D. and Caruthers, M. H. J. Am. Chem. Soc., 1981, 103, 3185-3191;Beaucage, S. L. and Caruthers, M. H. Tetrahedron Lett., 1981, 22,1859-1862; Dahl, B. J., et al., Acta Chem. Scand,. 1990, 44, 639-641;Reddy, M. P., et al., Tetrahedrom Lett., 1994, 25, 4311-4314; Wincott,F. et al., Nucleic Acids Res., 1995, 23, 2677-2684; Griffin, B. E., etal., Tetrahedron, 1967, 23, 2301-2313; Griffin, B. E., et al.,Tetrahedron, 1967, 23, 2315-2331).

RNA antisense oligonucleotides (RNA oligonucleotides) of the presentinvention can be synthesized by the methods herein or purchased fromDharmacon Research, Inc (Lafayette, Colo.). Once synthesized,complementary RNA antisense oligonucleotides can then be annealed bymethods known in the art to form double stranded (duplexed) antisenseoligonucleotides. For example, duplexes can be formed by combining 30 μlof each of the complementary strands of RNA oligonucleotides (50 uM RNAoligonucleotide solution) and 15 μl of 5× annealing buffer (100 mMpotassium acetate, 30 mM HEPES-KOH pH 7.4, 2 mM magnesium acetate)followed by heating for 1 minute at 90° C., then 1 hour at 37° C. Theresulting duplexed antisense oligonucleotides can be used in kits,assays, screens, or other methods to investigate the role of a targetnucleic acid.

EXAMPLE 18

Synthesis of Chimeric Oligonucleotides

Chimeric oligonucleotides, oligonucleosides or mixedoligonucleotides/oligo-nucleosides of the invention can be of severaldifferent types. These include a first type wherein the “gap” segment oflinked nucleosides is positioned between 5′ and 3′ “wing” segments oflinked nucleosides and a second “open end” type wherein the “gap”segment is located at either the 3′ or the 5′ terminus of theoligonucleotide. Oligonucleotides of the first type are also known inthe art as “gapmers” or gapped oligonucleotides. Oligonucleotides of thesecond type are also known in the art as “hemimers” or “wingmers”.

[2′-O-Me]-[2′-deoxy]-[2′-O-Me] Chimeric PhosphorothioateOligonucleotides

Chimeric oligonucleotides having 2′-O-alkyl phosphorothioate and2′-deoxy phosphorothioate oligonucleotide segments are synthesized usingan Applied Biosystems automated DNA synthesizer Model 394, as above.Oligonucleotides are synthesized using the automated synthesizer and2′-deoxy-5′-dimethoxytrityl-3′-O-phosphoramidite for the DNA portion and5′-dimethoxytrityl-2′-O-methyl-3′-O-phosphoramidite for 5′ and 3′ wings.The standard synthesis cycle is modified by incorporating coupling stepswith increased reaction times for the5′-dimethoxytrityl-2′-O-methyl-3′-O-phosphoramidite. The fully protectedoligonucleotide is cleaved from the support and deprotected inconcentrated ammonia (NH₄OH) for 12-16 hr at 55° C. The deprotectedoligo is then recovered by an appropriate method (precipitation, columnchromatography, volume reduced in vacuo and analyzedspetrophotometrically for yield and for purity by capillaryelectrophoresis and by mass spectrometry.

[2′-O-(2-Methoxyethyl)]-[2′-deoxy]-[2′-O-(Methoxyethyl)] ChimericPhosphorothioate Oligonucleotides

[2′-O-(2-methoxyethyl)]-[2′-deoxy]-[2′-O-(methoxyethyl)] chimericphosphorothioate oligonucleotides were prepared as per the procedureabove for the 2′-O-methyl chimeric oligonucleotide, with thesubstitution of 2′-O-(methoxyethyl) amidites for the 2′-O-methylamidites.

[2′-O-(2-Methoxyethyl)Phosphodiester]-[2′-deoxyPhosphorothioate]-[2′-O-(2-Methoxyethyl) Phosphodiester] ChimericOligonucleotides

[2′-O-(2-methoxyethyl phosphodiester]-[2′-deoxyphosphorothioate]-[2′-O-(methoxyethyl) phosphodiester] chimericoligonucleotides are prepared as per the above procedure for the2′-O-methyl chimeric oligonucleotide with the substitution of2′-O-(methoxyethyl) amidites for the 2′-O-methyl amidites, oxidationwith iodine to generate the phosphodiester internucleotide linkageswithin the wing portions of the chimeric structures and sulfurizationutilizing 3,H-1,2 benzodithiole-3-one 1,1 dioxide (Beaucage Reagent) togenerate the phosphorothioate internucleotide linkages for the centergap.

Other chimeric oligonucleotides, chimeric oligonucleosides and mixedchimeric oligonucleotides/oligonucleosides are synthesized according toU.S. Pat. No. 5,623,065, herein incorporated by reference.

EXAMPLE 19

Design and Screening of Duplexed Antisense Oligonucleotides Directed toa Selected Target

In one aspect of the present invention, compositions comprising a seriesof nucleic acid duplexes and their complements can be designed to aparticular nucleic acid target. The ends of the strands may be modifiedby the addition of one or more natural or modified nucleobases to forman overhang. The sense strand of these compositions is then designed andsynthesized as the complement of the antisense strand and may alsocontain modifications or additions to either terminus. For example, inone embodiment, both strands of the complexes would be complementaryover the central nucleobases, each having overhangs at one or bothtermini.

For example, a duplex comprising an antisense oligonucleotide having thesequence CGAGAGGCGGACGGGACCG (SEQ ID NO.: 1) and having a two-nucleobaseoverhang of deoxythymidine(dT) would have the following structure:

SEQ ID NO.     cgagaggcggacgggaccgdTdT Antisense Strand 2    ||||||||||||||||||| dTdTgctctccgcctgccctggc Complement Strand 3

RNA strands of the duplex can be synthesized by methods disclosed hereinor purchased from Dharmacon Research Inc., (Lafayette, Colo.). Oncesynthesized, the complementary strands are annealed. The single strandsare aliquoted and diluted to a concentration of 50 uM. Once diluted, 30uL of each strand is combined with 15uL of a 5× solution of annealingbuffer. The final concentration of said buffer is 100 mM potassiumacetate, 30 mM HEPES-KOH pH 7.4, and 2 mM magnesium acetate. The finalvolume is 75 uL. This solution is incubated for 1 minute at 90° C. andthen centrifuged for 15 seconds. The tube is allowed to sit for 1 hourat 37° C. at which time the dsRNA duplexes are used in experimentation.The final concentration of the dsRNA duplex is 20 uM. This solution canbe stored frozen (−20° C.) and freeze-thawed up to 5 times.

Once prepared, the duplexed antisense oligonucleotides are evaluated fortheir ability to modulate a target expression.

When cells reached 80% confluency, they are treated with duplexedantisense compositions of the invention. For cells grown in 96-wellplates, wells are washed once with 200 μL OPTI-MEM-1 reduced-serummedium (Gibco BRL) and then treated with 130 μL of OPTI-MEM-1 containing12 μg/mL LIPOFECTIN (Gibco BRL) and the desired duplex antisenseoligonucleotide at a final concentration of 200 nM. After 5 hours oftreatment, the medium is replaced with fresh medium. Cells are harvested16 hours after treatment, at which time RNA is isolated and targetreduction measured by RT-PCR.

EXAMPLE 20

Oligonucleotide Isolation

After cleavage from the controlled pore glass solid support anddeblocking in concentrated ammonium hydroxide at 55° C. for 12-16 hours,the oligonucleotides or oligonucleosides are recovered by precipitationout of 1 M NH₄Ac with >3 volumes of ethanol. Synthesizedoligonucleotides were analyzed by electrospray mass spectroscopy(molecular weight determination) and by capillary gel electrophoresisand judged to be at least 70% full length material. The relative amountsof phosphorothioate and phosphodiester linkages obtained in thesynthesis was determined by the ratio of correct molecular weightrelative to the −16 amu product (+/−32 +/−48). For some studiesoligonucleotides were purified by HPLC, as described by Chiang et al.,J. Biol. Chem. 1991, 266, 18162-18171. Results obtained withHPLC-purified material were similar to those obtained with non-HPLCpurified material.

EXAMPLE 21

Oligonucleotide Synthesis—96 Well Plate Format

Oligonucleotides were synthesized via solid phase P(III) phosphoramiditechemistry on an automated synthesizer capable of assembling 96 sequencessimultaneously in a 96-well format. Phosphodiester internucleotidelinkages were afforded by oxidation with aqueous iodine.Phosphorothioate internucleotide linkages were generated bysulfurization utilizing 3,H-1,2 benzodithiole-3-one 1,1 dioxide(Beaucage Reagent) in anhydrous acetonitrile. Standard base-protectedbeta-cyanoethyl-diiso-propyl phosphoramidites were purchased fromcommercial vendors (e.g. PE-Applied Biosystems, Foster City, Calif., orPharmacia, Piscataway, N.J.). Non-standard nucleosides are synthesizedas per standard or patented methods. They are utilized as base protectedbeta-cyanoethyldiisopropyl phosphoramidites.

Oligonucleotides were cleaved from support and deprotected withconcentrated NH₄OH at elevated temperature (55-60° C.) for 12-16 hoursand the released product then dried in vacuo. The dried product was thenre-suspended in sterile water to afford a master plate from which allanalytical and test plate samples are then diluted utilizing roboticpipettors.

EXAMPLE 22

Oligonucleotide Analysis Using 96-Well Plate Format

The concentration of oligonucleotide in each well was assessed bydilution of samples and UV absorption spectroscopy. The full-lengthintegrity of the individual products was evaluated by capillaryelectrophoresis (CE) in either the 96-well format (Beckman P/ACE™ MDQ)or, for individually prepared samples, on a commercial CE apparatus(e.g., Beckman P/ACE™ 5000, ABI 270). Base and backbone composition wasconfirmed by mass analysis of the oligonucleotides utilizingelectrospray-mass spectroscopy. All assay test plates were diluted fromthe master plate using single and multi-channel robotic pipettors.Plates were judged to be acceptable if at least 85% of theoligonucleotides on the plate were at least 85% full length.

EXAMPLE 23

Cell Culture and Oligonucleotide Treatment

The effect of oligonucleotides on target nucleic acid expression can betested in any of a variety of cell types provided that the targetnucleic acid is present at measurable levels. This can be routinelydetermined using, for example, PCR or Northern blot analysis. Thefollowing cell types are provided for illustrative purposes, but othercell types can be routinely used, provided that the target is expressedin the cell type chosen. This can be readily determined by methodsroutine in the art, for example Northern blot analysis, ribonucleaseprotection assays, or RT-PCR.

T-24 Cells:

The human transitional cell bladder carcinoma cell line T-24 wasobtained from the American Type Culture Collection (ATCC) (Manassas,Va.). T-24 cells were routinely cultured in complete McCoy's 5A basalmedia (Invitrogen Corporation, Carlsbad, Calif. or Gibco/LifeTechnologies, Gaithersburg, Md.) supplemented with 10% fetal calf serum(Invitrogen Corporation, Carlsbad, Calif. or Gibco/Life Technologies,Gaithersburg, Md.), penicillin 100 units per mL, and streptomycin 100micrograms per mL (Invitrogen Corporation, Carlsbad, Calif. orGibco/Life Technologies, Gaithersburg, Md.). Cells were routinelypassaged by trypsinization and dilution when they reached 90%confluence. Cells were seeded into 96-well plates (Falcon-Primaria#353872) at a density of 7000 cells/well for use in RT-PCR analysis.

For Northern blotting or other analysis, cells may be seeded onto 100 mmor other standard tissue culture plates and treated similarly, usingappropriate volumes of medium and oligonucleotide.

A549 Cells:

The human lung carcinoma cell line A549 was obtained from the AmericanType Culture Collection (ATCC) (Manassas, Va.). A549 cells wereroutinely cultured in DMEM basal media (Invitrogen Corporation,Carlsbad, Calif. or Gibco/Life Technologies, Gaithersburg, Md.)supplemented with 10% fetal calf serum (Invitrogen Corporation,Carlsbad, Calif. or Gibco/Life Technologies, Gaithersburg, Md.),penicillin 100 units per mL, and streptomycin 100 micrograms per mL(Invitrogen Corporation, Carlsbad, Calif. or Gibco/Life Technologies,Gaithersburg, Md.). Cells were routinely passaged by trypsinization anddilution when they reached 90% confluence.

NHDF Cells:

Human neonatal dermal fibroblast (NHDF) were obtained from the CloneticsCorporation (Walkersville, Md.). NHDFs were routinely maintained inFibroblast Growth Medium (Clonetics Corporation, Walkersville, Md.)supplemented as recommended by the supplier. Cells were maintained forup to 10 passages as recommended by the supplier.

HEK Cells:

Human embryonic keratinocytes (HEK) were obtained from the CloneticsCorporation (Walkersville, Md.). HEKs were routinely maintained inKeratinocyte Growth Medium (Clonetics Corporation, Walkersville, Md.)formulated as recommended by the supplier. Cells were routinelymaintained for up to 10 passages as recommended by the supplier.

3T3-L1 Cells:

The mouse embryonic adipocyte-like cell line 3T3-L1 was obtained fromthe American Type Culure Collection (Manassas, Va.). 3T3-L1 cells wereroutinely cultured in DMEM, high glucose (Gibco/Life Technologies,Gaithersburg, Md.) supplemented with 10% fetal calf serum (Gibco/LifeTechnologies, Gaithersburg, Md.). Cells were routinely passaged bytrypsinization and dilution when they reached 80% confluence. Cells wereseeded into 96-well plates (Falcon-Primaria #3872) at a density of 4000cells/well for use in RT-PCR analysis.

For Northern blotting or other analyses, cells may be seeded onto 100 mmor other standard tissue culture plates and treated similarly, usingappropriate volumes of medium and oligonucleotide.

Treatment with Oligonucleotides:

When cells reached 65-80% confluency, they were treated witholigonucleotide. For cells grown in 96-well plates, wells were washedonce with 100 μL OPTI-MEM™-1 reduced-serum medium (InvitrogenCorporation, Carlsbad, Calif.) and then treated with 130 μL ofOPTI-MEM™-1 containing 3.75 μg/mL LIPOFECTIN™ (Invitrogen Corporation,Carlsbad, Calif.) and the desired concentration of oligonucleotide.Cells are treated and data are obtained in triplicate. After 4-7 hoursof treatment at 37° C., the medium was replaced with fresh medium. Cellswere harvested 16-24 hours after oligonucleotide treatment.

The concentration of oligonucleotide used varies from cell line to cellline. To determine the optimal oligonucleotide concentration for aparticular cell line, the cells are treated with a positive controloligonucleotide at a range of concentrations. For human cells thepositive control oligonucleotide is selected from either ISIS 13920(TCCGTCATCGCTCCTCAGGG, SEQ ID NO: 150) which is targeted to human H-ras,or ISIS 18078, (GTGCGCGCGAGCCCGAAATC, SEQ ID NO: 151) which is targetedto human Jun-N-terminal kinase-2 (JNK2). Both controls are2′-O-methoxyethyl gapmers (2′-O-methoxyethyls shown in bold) with aphosphorothioate backbone. For mouse or rat cells the positive controloligonucleotide is ISIS 15770, ATGCATTCTGCCCCCAAGGA, SEQ ID NO: 152, a2′-O-methoxyethyl gapmer (2′-O-methoxyethyls shown in bold) with aphosphorothioate backbone which is targeted to both mouse and rat c-raf.The concentration of positive control oligonucleotide that results in80% inhibition of c-H-ras (for ISIS 13920), JNK2 (for ISIS 18078) orc-raf (for ISIS 15770) mRNA is then utilized as the screeningconcentration for new oligonucleotides in subsequent experiments forthat cell line. If 80% inhibition is not achieved, the lowestconcentration of positive control oligonucleotide that results in 60%inhibition of c-H-ras, JNK2 or c-raf mRNA is then utilized as theoligonucleotide screening concentration in subsequent experiments forthat cell line. If 60% inhibition is not achieved, that particular cellline is deemed as unsuitable for oligonucleotide transfectionexperiments. The concentrations of antisense oligonucleotides usedherein are from 50 nM to 300 nM.

EXAMPLE 24

Analysis of Oligonucleotide Inhibition of a Target Expression

Antisense modulation of a target expression can be assayed in a varietyof ways known in the art. For example, a target mRNA levels can bequantitated by, e.g., Northern blot analysis, competitive polymerasechain reaction (PCR), or real-time PCR (RT-PCR). Real-time quantitativePCR is presently preferred. RNA analysis can be performed on totalcellular RNA or poly(A)+ mRNA. The preferred method of RNA analysis ofthe present invention is the use of total cellular RNA as described inother examples herein. Methods of RNA isolation are well known in theart. Northern blot analysis is also routine in the art. Real-timequantitative (PCR) can be conveniently accomplished using thecommercially available ABI PRISM™ 7600, 7700, or 7900 Sequence DetectionSystem, available from PE-Applied Biosystems, Foster City, Calif. andused according to manufacturer's instructions.

Protein levels of a target can be quantitated in a variety of ways wellknown in the art, such as immunoprecipitation, Western blot analysis(immunoblotting), enzyme-linked immunosorbent assay (ELISA) orfluorescence-activated cell sorting (FACS). Antibodies directed to atarget can be identified and obtained from a variety of sources, such asthe MSRS catalog of antibodies (Aerie Corporation, Birmingham, Mich.),or can be prepared via conventional monoclonal or polyclonal antibodygeneration methods well known in the art. See, for example, Ausubel, F.M. et al., Current Protocols in Molecular Biology, Volume 2, pp.11.12.1-11.12.9, John Wiley & Sons, Inc., 1997. Preparation ofmonoclonal antibodies is taught in, for example, Ausubel, F. M. et al.,Current Protocols in Molecular Biology, Volume 2, pp. 11.4.1-11.11.5,John Wiley & Sons, Inc., 1997.

Immunoprecipitation methods are standard in the art and can be found at,for example, Ausubel, F. M. et al., Current Protocols in MolecularBiology, Volume 2, pp. 10.16.1-10.16.11, John Wiley & Sons, Inc., 1998.Western blot (immunoblot) analysis is standard in the art and can befound at, for example, Ausubel, F. M. et al., Current Protocols inMolecular Biology, Volume 2, pp. 10.8.1-10.8.21, John Wiley & Sons,Inc., 1997. Enzyme-linked immunosorbent assays (ELISA) are standard inthe art and can be found at, for example, Ausubel, F. M. et al., CurrentProtocols in Molecular Biology, Volume 2, pp. 11.2.1-11.2.22, John Wiley& Sons, Inc., 1991.

EXAMPLE 25

Design of Phenotypic Assays and In Vivo Studies for the use of TargetInhibitors Phenotypic Assays

Once a target inhibitors have been identified by the methods disclosedherein, the oligonucleotides are further investigated in one or morephenotypic assays, each having measurable endpoints predictive ofefficacy in the treatment of a particular disease state or condition.

Phenotypic assays, kits and reagents for their use are well known tothose skilled in the art and are herein used to investigate the roleand/or association of a target in health and disease. Representativephenotypic assays, which can be purchased from any one of severalcommercial vendors, include those for determining cell viability,cytotoxicity, proliferation or cell survival (Molecular Probes, Eugene,Oreg.; PerkinElmer, Boston, Mass.), protein-based assays includingenzymatic assays (Panvera, LLC, Madison, Wis.; BD Biosciences, FranklinLakes, N.J.; Oncogene Research Products, San Diego, Calif.), cellregulation, signal transduction, inflammation, oxidative processes andapoptosis (Assay Designs Inc., Ann Arbor, Mich.), triglycerideaccumulation (Sigma-Aldrich, St. Louis, Mo.), angiogenesis assays, tubeformation assays, cytokine and hormone assays and metabolic assays(Chemicon International Inc., Temecula, Calif.; Amersham Biosciences,Piscataway, N.J.).

In one non-limiting example, cells determined to be appropriate for aparticular phenotypic assay (i.e., MCF-7 cells selected for breastcancer studies; adipocytes for obesity studies) are treated with atarget inhibitors identified from the in vitro studies as well ascontrol compounds at optimal concentrations which are determined by themethods described above. At the end of the treatment period, treated anduntreated cells are analyzed by one or more methods specific for theassay to determine phenotypic outcomes and endpoints.

Phenotypic endpoints include changes in cell morphology over time ortreatment dose as well as changes in levels of cellular components suchas proteins, lipids, nucleic acids, hormones, saccharides or metals.Measurements of cellular status which include pH, stage of the cellcycle, intake or excretion of biological indicators by the cell, arealso endpoints of interest.

Analysis of the geneotype of the cell (measurement of the expression ofone or more of the genes of the cell) after treatment is also used as anindicator of the efficacy or potency of the a target inhibitors.Hallmark genes, or those genes suspected to be associated with aspecific disease state, condition, or phenotype, are measured in bothtreated and untreated cells.

In Vivo Studies

The individual subjects of the in vivo studies described herein arewarm-blooded vertebrate animals, which includes humans. The clinicaltrial is subjected to rigorous controls to ensure that individuals arenot unnecessarily put at risk and that they are fully informed abouttheir role in the study.

To account for the psychological effects of receiving treatments,volunteers are randomly given placebo or a target inhibitor.Furthermore, to prevent the doctors from being biased in treatments,they are not informed as to whether the medication they areadministering is a a target inhibitor or a placebo. Using thisrandomization approach, each volunteer has the same chance of beinggiven either the new treatment or the placebo.

Volunteers receive either the a target inhibitor or placebo for eightweek period with biological parameters associated with the indicateddisease state or condition being measured at the beginning (baselinemeasurements before any treatment), end (after the final treatment), andat regular intervals during the study period. Such measurements includethe levels of nucleic acid molecules encoding a target or a targetprotein levels in body fluids, tissues or organs compared topre-treatment levels. Other measurements include, but are not limitedto, indices of the disease state or condition being treated, bodyweight, blood pressure, serum titers of pharmacologic indicators ofdisease or toxicity as well as ADME (absorption, distribution,metabolism and excretion) measurements. Information recorded for eachpatient includes age (years), gender, height (cm), family history ofdisease state or condition (yes/no), motivation rating(some/moderate/great) and number and type of previous treatment regimensfor the indicated disease or condition.

Volunteers taking part in this study are healthy adults (age 18 to 65years) and roughly an equal number of males and females participate inthe study. Volunteers with certain characteristics are equallydistributed for placebo and a target inhibitor treatment. In general,the volunteers treated with placebo have little or no response totreatment, whereas the volunteers treated with the a target inhibitorshow positive trends in their disease state or condition index at theconclusion of the study.

EXAMPLE 26

RNA Isolation

Poly(A)+ mRNA Isolation

Poly(A)+ mRNA was isolated according to Miura et al., (Clin. Chem.,1996, 42, 1758-1764). Other methods for poly(A)+ mRNA isolation areroutine in the art. Briefly, for cells grown on 96-well plates, growthmedium was removed from the cells and each well was washed with 200 μLcold PBS. 60 μL lysis buffer (10 mM Tris-HCl, pH 7.6, 1 mM EDTA, 0.5 MNaCl, 0.5% NP-40, 20 mM vanadyl-ribonucleoside complex) was added toeach well, the plate was gently agitated and then incubated at roomtemperature for five minutes. 55 μL of lysate was transferred to Oligod(T) coated 96-well plates (AGCT Inc., Irvine Calif.). Plates wereincubated for 60 minutes at room temperature, washed 3 times with 200 μLof wash buffer (10 mM Tris-HC1 pH 7.6, 1 mM EDTA, 0.3 M NaCl). After thefinal wash, the plate was blotted on paper towels to remove excess washbuffer and then air-dried for 5 minutes. 60 μL of elution buffer (5 mMTris-HCl pH 7.6), preheated to 70° C., was added to each well, the platewas incubated on a 90° C. hot plate for 5 minutes, and the eluate wasthen transferred to a fresh 96-well plate.

Cells grown on 100 mm or other standard plates may be treated similarly,using appropriate volumes of all solutions.

Total RNA Isolation

Total RNA was isolated using an RNEASY 96™ kit and buffers purchasedfrom Qiagen Inc. (Valencia, Calif.) following the manufacturer'srecommended procedures. Briefly, for cells grown on 96-well plates,growth medium was removed from the cells and each well was washed with200 μL cold PBS. 150 μL Buffer RLT was added to each well and the platevigorously agitated for 20 seconds. 150 μL of 70% ethanol was then addedto each well and the contents mixed by pipetting three times up anddown. The samples were then transferred to the RNEASY 96™ well plateattached to a QIAVAC™ manifold fitted with a waste collection tray andattached to a vacuum source. Vacuum was applied for 1 minute. 500 μL ofBuffer RW1 was added to each well of the RNEASY 96™ plate and incubatedfor 15 minutes and the vacuum was again applied for 1 minute. Anadditional 500 μL of Buffer RW1 was added to each well of the RNEASY 96™plate and the vacuum was applied for 2 minutes. 1 mL of Buffer RPE wasthen added to each well of the RNEASY 96™ plate and the vacuum appliedfor a period of 90 seconds. The Buffer RPE wash was then repeated andthe vacuum was applied for an additional 3 minutes. The plate was thenremoved from the QIAVAC™ manifold and blotted dry on paper towels. Theplate was then re-attached to the QIAVAC™ manifold fitted with acollection tube rack containing 1.2 mL collection tubes. RNA was theneluted by pipetting 140 μL of RNAse free water into each well,incubating 1 minute, and then applying the vacuum for 3 minutes.

The repetitive pipetting and elution steps may be automated using aQIAGEN Bio-Robot 9604 (Qiagen, Inc., Valencia Calif.). Essentially,after lysing of the cells on the culture plate, the plate is transferredto the robot deck where the pipetting, DNase treatment and elution stepsare carried out.

EXAMPLE 27

Real-time Quantitative PCR Analysis of a Target mRNA Levels

Quantitation of a target mRNA levels was accomplished by real-timequantitative PCR using the ABI PRISM™ 7600, 7700, or 7900 SequenceDetection System (PE-Applied Biosystems, Foster City, Calif.) accordingto manufacturer's instructions. This is a closed-tube, non-gel-based,fluorescence detection system which allows high-throughput quantitationof polymerase chain reaction (PCR) products in real-time. As opposed tostandard PCR in which amplification products are quantitated after thePCR is completed, products in real-time quantitative PCR are quantitatedas they accumulate. This is accomplished by including in the PCRreaction an oligonucleotide probe that anneals specifically between theforward and reverse PCR primers, and contains two fluorescent dyes. Areporter dye (e.g., FAM or JOE, obtained from either PE-AppliedBiosystems, Foster City, Calif., Operon Technologies Inc., Alameda,Calif. or Integrated DNA Technologies Inc., Coralville, Iowa) isattached to the 5′ end of the probe and a quencher dye (e.g., TAMRA,obtained from either PE-Applied Biosystems, Foster City, Calif., OperonTechnologies Inc., Alameda, Calif. or Integrated DNA Technologies Inc.,Coralville, Iowa) is attached to the 3′ end of the probe. When the probeand dyes are intact, reporter dye emission is quenched by the proximityof the 3′ quencher dye. During amplification, annealing of the probe tothe target sequence creates a substrate that can be cleaved by the5′-exonuclease activity of Taq polymerase. During the extension phase ofthe PCR amplification cycle, cleavage of the probe by Taq polymerasereleases the reporter dye from the remainder of the probe (and hencefrom the quencher moiety) and a sequence-specific fluorescent signal isgenerated. With each cycle, additional reporter dye molecules arecleaved from their respective probes, and the fluorescence intensity ismonitored at regular intervals by laser optics built into the ABI PRISM™Sequence Detection System. In each assay, a series of parallel reactionscontaining serial dilutions of mRNA from untreated control samplesgenerates a standard curve that is used to quantitate the percentinhibition after antisense oligonucleotide treatment of test samples.

Prior to quantitative PCR analysis, primer-probe sets specific to thetarget gene being measured are evaluated for their ability to be“multiplexed” with a GAPDH amplification reaction. In multiplexing, boththe target gene and the internal standard gene GAPDH are amplifiedconcurrently in a single sample. In this analysis, mRNA isolated fromuntreated cells is serially diluted. Each dilution is amplified in thepresence of primer-probe sets specific for GAPDH only, target gene only(“single-plexing”), or both (multiplexing). Following PCR amplification,standard curves of GAPDH and target mRNA signal as a function ofdilution are generated from both the single-plexed and multiplexedsamples. If both the slope and correlation coefficient of the GAPDH andtarget signals generated from the multiplexed samples fall within 10% oftheir corresponding values generated from the single-plexed samples, theprimer-probe set specific for that target is deemed multiplexable. Othermethods of PCR are also known in the art.

PCR reagents were obtained from Invitrogen Corporation, (Carlsbad,Calif.). RT-PCR reactions were carried out by adding 20 μL PCR cocktail(2.5×PCR buffer minus MgCl₂, 6.6 mM MgCl₂, 375 μM each of dATP, dCTP,dCTP and dGTP, 375 nM each of forward primer and reverse primer, 125 nMof probe, 4 Units RNAse inhibitor, 1.25 Units PLATINUM® Taq, 5 UnitsMuLV reverse transcriptase, and 2.5×ROX dye) to 96-well platescontaining 30 μL total RNA solution (20-200 ng). The RT reaction wascarried out by incubation for 30 minutes at 48° C. Following a 10 minuteincubation at 95° C. to activate the PLATINUM® Taq, 40 cycles of atwo-step PCR protocol were carried out: 95° C. for 15 seconds(denaturation) followed by 60° C. for 1.5 minutes (annealing/extension).

Gene target quantities obtained by real time RT-PCR are normalized usingeither the expression level of GAPDH, a gene whose expression isconstant, or by quantifying total RNA using RiboGreen™ (MolecularProbes, Inc. Eugene, Oreg.). GAPDH expression is quantified by real timeRT-PCR, by being run simultaneously with the target, multiplexing, orseparately. Total RNA is quantified using RiboGreen™ RNA quantificationreagent (Molecular Probes, Inc. Eugene, Oreg.). Methods of RNAquantification by RiboGreen™ are taught in Jones, L. J., et al,(Analytical Biochemistry, 1998, 265, 368-374).

In this assay, 170 μL of RiboGreen™ working reagent (RiboGreen™ reagentdiluted 1:350 in 10 mM Tris-HCl, 1 mM EDTA, pH 7.5) is pipetted into a96-well plate containing 30 μL purified, cellular RNA. The plate is readin a CytoFluor 4000 (PE Applied Biosystems) with excitation at 485 nmand emission at 530 nm.

Probes and are designed to hybridize to a human a target sequence, usingpublished sequence information.

Concerning Survivin as the target, PCR reagents were obtained fromPE-Applied Biosystems, Foster City, Calif. RT-PCR reactions were carriedout by adding 25 μL PCR cocktail (1×TAQMAN buffer A, 5.5 mM MgCl₂, 300μM each of dATP, dCTP and dGTP, 600 μM of dUTP, 100 nM each of forwardprimer, reverse primer, and probe, 20 Units RNAse inhibitor, 1.25 UnitsAMPLITAQ GOLD, and 12.5 Units MuLV reverse transcriptase) to 96 wellplates containing 25 μL poly(A) mRNA solution. The RT reaction wascarried out by incubation for 30 minutes at 48° C. Following a 10 minuteincubation at 95° C. to activate the AMPLITAQ GOLD, 40 cycles of atwo-step PCR protocol were carried out: 95° C. for 15 seconds(denaturation) followed by 60° C. for 1.5 minutes (annealing/extension).Probes and primers to human Survivin were designed to hybridize to ahuman Survivin sequence, using published sequence information (GenBankaccession number U75285, incorporated herein as SEQ ID NO: 153). Forhuman Survivin the PCR primers were:

-   forward primer: AAGGACCACCGCATCTCTACA (SEQ ID NO: 154)    reverse primer: CCAAGTCTGGCTCGTTCTCAGT (SEQ ID NO: 5) and the PCR    probe was: FAM-CGAGGCTGGCTTCATCCACTGCC-TAMRA (SEQ ID NO: 6) where    FAM (PE-Applied Biosystems, Foster City, Calif.) is the fluorescent    reporter dye) and TAMRA (PE-Applied Biosystems, Foster City, Calif.)    is the quencher dye. For human GAPDH the PCR primers were:-   forward primer: GAAGGTGAAGGTCGGAGTC (SEQ ID NO: 7)    reverse primer: GAAGATGGTGATGGGATTTC (SEQ ID NO: 155) and the PCR    probe was: 5′ JOE-CAAGCTTCCCGTTCTCAGCC-TAMRA 3′ (SEQ ID NO: 156)    where JOE (PE-Applied Biosystems, Foster City, Calif.) is the    fluorescent reporter dye) and TAMRA (PE-Applied Biosystems, Foster    City, Calif.) is the quencher dye.

EXAMPLE 28

Northern Blot Analysis of a Target mRNA Levels

Eighteen hours after antisense treatment, cell monolayers were washedtwice with cold PBS and lysed in 1 mL RNAZOL™ (TEL-TEST “B” Inc.,Friendswood, Tex.). Total RNA was prepared following manufacturer'srecommended protocols. Twenty micrograms of total RNA was fractionatedby electrophoresis through 1.2% agarose gels containing 1.1%formaldehyde using a MOPS buffer system (AMRESCO, Inc. Solon, Ohio). RNAwas transferred from the gel to HYBOND™−N+ nylon membranes (AmershamPharmacia Biotech, Piscataway, N.J.) by overnight capillary transferusing a Northern/Southern Transfer buffer system (TEL-TEST “B” Inc.,Friendswood, Tex.). RNA transfer was confirmed by UV visualization.Membranes were fixed by UV cross-linking using a STRATALINKER™ UVCrosslinker 2400 (Stratagene, Inc, La Jolla, Calif.) and then probedusing QUICKHYB™ hybridization solution (Stratagene, La Jolla, Calif.)using manufacturer's recommendations for stringent conditions.

To detect human a target, a human a target specific primer probe set isprepared by PCR To normalize for variations in loading and transferefficiency membranes are stripped and probed for humanglyceraldehyde-3-phosphate dehydrogenase (GAPDH) RNA (Clontech, PaloAlto, Calif.).

Hybridized membranes were visualized and quantitated using aPHOSPHORIMAGER™ and IMAGEQUANT™ Software V3.3 (Molecular Dynamics,Sunnyvale, Calif.). Data was normalized to GAPDH levels in untreatedcontrols.

To detect human Survivin, for example, a human Survivin specific probewas prepared by PCR using the forward primer AAGGACCACCGCATCTCTACA (SEQID NO: 157) and the reverse primer CCAAGTCTGGCTCGTTCTCAGT (SEQ ID NO:5). To normalize for variations in loading and transfer efficiencymembranes were stripped and probed for human glyceraldehyde-3-phosphatedehydrogenase (GAPDH) RNA (Clontech, Palo Alto, Calif.).

EXAMPLE 29

Inhibition of Human a Target Expression by Oligonucleotides

In accordance with the present invention, a series of compositions aredesigned to target different regions of the human target RNA. Theoligonucleotides are analyzed for their effect on human target mRNAlevels by quantitative real-time PCR as described in other examplesherein. Data are averages from three experiments. The target regions towhich these preferred sequences are complementary are herein referred toas “preferred target segments” and are therefore preferred for targetingby compositions of the present invention. The sequences represent thereverse complement of the preferred compositions.

As these “preferred target segments” have been found by experimentationto be open to, and accessible for, hybridization with the compositionsof the present invention, one of skill in the art will recognize or beable to ascertain, using no more than routine experimentation, furtherembodiments of the invention that encompass other compositions thatspecifically hybridize to these preferred target segments andconsequently inhibit the expression of a target.

According to the present invention, compositions include antisenseoligonucleotides, antisense oligonucleotides, asRNA's (single strandthat may include a double stranded region), siRNA's (double stranded orsingle stranded with a double stranded region), ribozymes, externalguide sequence (EGS) oligonucleotides, alternate splicers, primers,probes, and other short oligonucleotides which hybridize to at least aportion of the target nucleic acid.

EXAMPLE 30

Modulation of Human Survivin Expression by Double Stranded RNA (dsRNA)

In accordance with the present invention, a series of double strandedoligomeric compounds comprising the antisense compounds of the presentinvention and their complements thereof, were designed to targetsurvivin mRNA. The oligomeric compounds were evaluated in HeLa cells.Culture methods used for HeLa cells are found, for example, athttp://www.atcc.org.

For cells grown in 96-well plates, wells were washed once with 200 μLOPTI-MEM-1™ reduced-serum medium (Gibco BRL) and then treated with 130μL of OPTI-MEM-1™ containing 12 μg/mL LIPOFECTIN™ (Gibco BRL) and thedesired dsRNA at a final concentration of 25 nM. After 5 hours oftreatment, the medium was replaced with fresh medium. Cells wereharvested 16 hours after dsRNA treatment, at which time RNA was isolatedand target reduction measured by RT-PCR.

Prior to treatment of the HeLa cells, the dsRNA oligomers were generatedby annealing the antisense and sense strands according to the methodoutlined herein and known to those skilled in the art.

EXAMPLE 31

Western Blot Analysis of Target Protein Levels

Western blot analysis (immunoblot analysis) is carried out usingstandard methods. Cells are harvested 16-20 h after treatment witholigomeric comounds or compositions of the invention, washed once withPBS, suspended in Laemmli buffer (100 ul/well), boiled for 5 minutes andloaded on a 16% SDS-PAGE gel. Gels are run for 1.5 hours at 150 V, andtransferred to membrane for western blotting. Appropriate primaryantibody directed to a target is used, with a radiolabeled orfluorescently labeled secondary antibody directed against the primaryantibody species. Bands are visualized using a PHOSPHORIMAGER™(Molecular Dynamics, Sunnyvale Calif.).

EXAMPLE 32

Design and Screening of Duplexed Antisense Compounds Targeting Survivin

In accordance with the present invention, a series of nucleic acidduplexes comprising the antisense compounds of the present invention andtheir complements can be designed to target survivin. The nucleobasesequence of the antisense strand of the duplex comprises at least aportion of an oligonucleotide to survivin as described herein. The endsof the strands may be modified by the addition of one or more natural ormodified nucleobases to form an overhang. The sense strand of the dsRNAis then designed and synthesized as the complement of the antisensestrand and may also contain modifications or additions to eitherterminus. For example, in one embodiment, both strands of the dsRNAduplex would be complementary over the central nucleobases, each havingoverhangs at one or both termini.

For example, a duplex comprising an antisense strand having the sequenceCGAGAGGCGGACGGGACCG (SEQ ID NO: 1) and having a two-nucleobase overhangof deoxythymidine(dT) would have the following structure:

SEQ ID NO.     cgagaggcggacgggaccgdTdT Antisense Strand 2    ||||||||||||||||||| dTdTgctctccgcctgccctggc Complement Strand 3

In another embodiment, a duplex comprising an antisense strand havingthe same sequence CGAGAGGCGGACGGGACCG (SEQ ID NO: 10) may be preparedwith blunt ends (no single stranded overhang) as shown:

cgagaggcggacgggaccg Antisense Strand 1 |||||||||||||||||||gctctccgcctgccctggc Complement Strand 4

RNA strands of the duplex can be synthesized by methods disclosed hereinor purchased from Dharmacon Research Inc., (Lafayette, Colo.). Oncesynthesized, the complementary strands are annealed. The single strandsare aliquoted and diluted to a concentration of 50 uM. Once diluted, 30uL of each strand is combined with 15uL of a 5× solution of annealingbuffer. The final concentration of said buffer is 100 mM potassiumacetate, 30 mM HEPES-KOH pH 7.4, and 2 mM magnesium acetate. The finalvolume is 75 uL. This solution is incubated for 1 minute at 90° C. andthen centrifuged for 15 seconds. The tube is allowed to sit for 1 hourat 37° C. at which time the dsRNA duplexes are used in experimentation.The final concentration of the dsRNA duplex is 20 uM. This solution canbe stored frozen (−20° C.) and freeze-thawed up to 5 times.

Once prepared, the duplexed antisense compounds are evaluated for theirability to modulate survivin expression according to the protocolsdescribed herein.

EXAMPLE 33

Representative Cell Lines

MCF-7 Cells

The human breast carcinoma cell line MCF-7 is obtained from the AmericanType Culture Collection (Manassas, Va.). These cells contain a wild-typep53 gene. MCF-7 cells are routinely cultured in DMEM low glucose(Gibco/Life Technologies, Gaithersburg, Md.) supplemented with 10% fetalcalf serum (Gibco/Life Technologies, Gaithersburg, Md.). Cells areroutinely passaged by trypsinization and dilution when they reach 90%confluence. Cells are seeded into 96-well plates (Falcon-Primaria #3872)at a density of 7000 cells/well for treatment with the compositions ofthe invention.

HepB3 Cells

The human hepatoma cell line HepB3 (Hep3B2.1-7) is obtained from theAmerican Type Culture Collection (ATCC-ATCC Catalog # HB-8064)(Manassas, Va.). This cell line was initially derived from ahepatocellular carcinoma of an 8-yr-old black male. The cells areepithelial in morphology and are tumorigenic in nude mice. HepB3 cellsare routinely cultured in Minimum Essential Medium (MEM) with Earle'sBalanced Salt Solution, 2 mM L-glutamine, 1.5 g/L sodium bicarbonate,0.1 mM nonessential amino acids, 1.0 mM sodium pyruvate (ATCC #20-2003,Manassas, Va.) and with 10% heat-inactivated fetal bovine serum(Gibco/Life Technologies, Gaithersburg, Md.). Cells are routinelypassaged by trypsinization and dilution when they reach 90% confluence.

T-24 Cells

The transitional cell bladder carcinoma cell line T-24 is obtained fromthe American Type Culture Collection (ATCC) (Manassas, Va.). T-24 cellsare routinely cultured in complete McCoy's 5A basal media (Gibco/LifeTechnologies, Gaithersburg, Md.) supplemented with 10% fetal calf serum(Gibco/Life Technologies, Gaithersburg, Md.), penicillin 100 units permL, and streptomycin 100 μg/mL (Gibco/Life Technologies, Gaithersburg,Md.). Cells are routinely passaged by trypsinization and dilution whenthey reach 90% confluence. Cells are seeded into 96-well plates(Falcon-Primaria #3872) at a density of 7000 cells/well for treatmentwith the compound of the invention.

A549 Cells

The human lung carcinoma cell line A549 is obtained from the AmericanType Culture Collection (ATCC) (Manassas, Va.). A549 cells are routinelycultured in DMEM basal media (Gibco/Life Technologies, Gaithersburg,Md.) supplemented with 10% fetal calf serum (Gibco/Life Technologies,Gaithersburg, Md.), penicillin 100 units per mL, and streptomycin 100μg/mL (Gibco/Life Technologies, Gaithersburg, MD). Cells are routinelypassaged by trysinization and dilution when they reach 90% confluence.Cells are seeded into 96-well plates (Falcon-Primaria #3872) at adensity of 7000 cells/well for treatment with the compound of theinvention.

Primary Mouse Hepatocytes

Primary mouse hepatocytes are prepared from CD-1 mice purchased fromCharles River Labs. Primary mouse hepatocytes are routinely cultured inHepatocyte Attachment Media (Invitrogen Life Technologies, Carlsbad,Calif.) supplemented with 10% Fetal Bovine Serum (Invitrogen LifeTechnologies, Carlsbad, Calif.), 250 nM dexamethasone (Sigma-AldrichCorporation, St. Louis, Mo.), 10 nM bovine insulin (Sigma-AldrichCorporation, St. Louis, Mo.). Cells are seeded into 96-well plates(Falcon-Primaria #353872, BD Biosciences, Bedford, MA) at a density of4000-6000 cells/well for treatment with the compositions of theinvention.

EXAMPLE 34

Liposome-mediated Treatment with Compositions of the Invention

When cells reach the desired confluency, they can be treated with thecompositions of the invention by liposome-mediated transfection. Forcells grown in 96-well plates, wells are washed once with 200 μLOPTI-MEM™-1 reduced-serum medium (Gibco BRL) and then treated with 100μL of OPTI-MEM™-1 containing 2.5 μg/mL LIPOFECTIN™ (Gibco BRL) and thecompositions of the invention at the desired final concentration. After4 hours of treatment, the medium is replaced with fresh medium. Cellsare harvested 16 hours after treatment with the compositions of theinvention for target mRNA expression analysis by real-time PCR.

EXAMPLE 35

Electroporation-mediated Treatment with Compositions of the Invention

When the cells reach the desired confluency, they can be treated withthe compositions of the invention by electorporation. Cells areelectroporated in the presence of the desired concentration of anoligonucleotide of the invention in 1 mm cuvettes at a density of 1×10⁷cells/mL, a voltage of 75V and a pulse length of 6 ms. Following thedelivery of the electrical pulse, cells are replated for 16 to 24 hours.Cells are then harvested for target mRNA expression analysis byreal-time PCR.

EXAMPLE 36

Apoptosis Assay

Caspase-3 activity is evaluated with an fluorometric HTS Caspase-3 assay(Oncogene Research Products, San Diego, Calif.) that detects cleavageafter aspartate residues in the peptide sequence (DEVD). The DEVDsubstrate is labeled with a fluorescent molecule, which exhibits a blueto green shift in fluorescence upon cleavage. Active caspase-3 intreated cells is measured by this assay according to the manufacturer'sinstructions. Following treatment with the compositions of theinvention, 50 μL of assay buffer is added to each well, followed byaddition 20 μL of the caspase-3 fluorescent substrate conjugate. Dataare obtained in triplicate. Fluorescence in wells is immediatelydetected (excitation/emission 400/505 nm) using a fluorescent platereader (SpectraMAX GeminiXS, Molecular Devices, Sunnyvale, Calif.). Theplate is covered and incubated at 37° C. for an additional three hours,after which the fluorescence is again measured (excitation/emission400/505 nm). The value at time zero is subtracted from the measurementobtained at 3 hours. The measurement obtained from the untreated controlcells is designated as 100% activity.

EXAMPLE 37

Cell Proliferation and Viability Assay

Cell viability and proliferation are measured using the CyQuant CellProliferation Assay Kit (Molecular Probes, Eugene, Oreg.) utilizing theCyQuant GR green fluorescent dye which exhibits strong fluorescenceenhancement when bound to cellular nucleic acids. The assay is performedaccording to the manufacturer's instructions. After the treatment withone or more compositions of the invention, the microplate is gentlyinverted to remove the medium from the wells, which are each washed oncewith 200 μL of phosphate-buffered saline. Plates are frozen at −70° C.and then thawed. A volume of 200 μL of the CyQUANT GR dye/cell-lysisbuffer is added to each well. The microplate is incubated for 5 minutesat room temperature, protected from light. Data are obtained intriplicate. Fluorescence in wells is immediately detected(excitation/emission 480/520 nm) using a fluorescent plate reader(SpectraMAX GeminiXS, Molecular Devices, Sunnyvale, Calif.). Themeasurement obtained from the untreated control cells is designated as100% activity.

EXAMPLE 38

Leptin-deficient Mice: A Model of Obesity and Diabetes (ob/ob Mice)

Leptin is a hormone produced by fat that regulates appetite.Deficiencies in this hormone in both humans and non-human animals leadsto obesity. ob/ob mice have a mutation in the leptin gene which resultsin obesity and hyperglycemia. As such, these mice are a useful model forthe investigation of obesity and diabetes and treatments designed totreat these conditions. ob/ob mice have higher circulating levels ofinsulin and are less hyperglycemic than db/db mice, which harbor amutation in the leptin receptor. In accordance with the presentinvention, the compositions of the invention are tested in the ob/obmodel of obesity and diabetes.

Seven-week old male C57Bl/6J-Lepr ob/ob mice (Jackson Laboratory, BarHarbor, Me.) are fed a diet with a fat content of 10-15% and aresubcutaneously injected with the compositions of the invention or acontrol compound at a dose of 25 mg/kg two times per week for 4 weeks.Saline-injected animals, leptin wildtype littermates (i.e. leanlittermates) and ob/ob mice fed a standard rodent diet serve ascontrols. After the treatment period, mice are sacrificed and targetlevels are evaluated in liver, brown adipose tissue (BAT) and whiteadipose tissue (WAT). RNA isolation and target mRNA expression levelquantitation are performed as described by other examples herein.

To assess the physiological effects resulting from inhibition of targetmRNA, the ob/ob mice are further evaluated at the end of the treatmentperiod for serum lipids, serum free fatty acids, serum cholesterol(CHOL), liver triglycerides, fat tissue triglycerides and liver enzymelevels. Hepatic steatosis, or clearing of lipids from the liver, isassessed by measuring the liver triglyceride content. Hepatic steatosisis assessed by routine histological analysis of frozen liver tissuesections stained with oil red O stain, which is commonly used tovisualize lipid deposits, and counterstained with hematoxylin and eosin,to visualize nuclei and cytoplasm, respectively.

The effects of target inhibition on glucose and insulin metabolism areevaluated in the ob/ob mice treated with the compositions of theinvention. Plasma glucose is measured at the start of the treatment andafter 2 weeks and 4 weeks of treatment. Plasma insulin is similarlymeasured at the beginning of the treatment, and following at 2 weeks andat 4 weeks of treatment. Glucose and insulin tolerance tests are alsoadministered in fed and fasted mice. Mice receive intraperitonealinjections of either glucose or insulin, and the blood glucose andinsulin levels are measured before the insulin or glucose challenge andat 15, 20 or 30 minute intervals for up to 3 hours.

To assess the metabolic rate of ob/ob mice treated with the compositionsof the invention, the respiratory quotient and oxygen consumption of themice are also measured.

The ob/ob mice that received treatment are further evaluated at the endof the treatment period for the effects of target inhibition on theexpression genes that participate in lipid metabolism, cholesterolbiosynthesis, fatty acid oxidation, fatty acid storage, gluconeogenesisand glucose metabolism. These genes include, but are not limited to,HMG-CoA reductase, acetyl-CoA carboxylase 1 and acetyl-CoA carboxylase2, carnitine palmitoyltransferase I and glycogen phosphorylase,glucose-6-phosphatase and phosphoenolpyruvate carboxykinase 1,lipoprotein lipase and hormone sensitive lipase. mRNA levels in liverand white and brown adipose tissue are quantitated by real-time PCR asdescribed in other examples herein, employing primer-probe sets that aregenerated using published sequences of each gene of interest.

EXAMPLE 39

Leptin Receptor-deficient Mice: A Model of Obesity and Diabetes (db/dbMice)

Leptin is a hormone produced by fat that regulates appetite.Deficiencies in this hormone in both humans and non-human animals leadsto obesity. db/db mice have a mutation in the leptin receptor gene whichresults in obesity and hyperglycemia. As such, these mice are a usefulmodel for the investigation of obesity and diabetes and treatmentsdesigned to treat these conditions. db/db mice, which have lowercirculating levels of insulin and are more hyperglycemic than ob/ob micewhich harbor a mutation in the leptin gene, are often used as a rodentmodel of type 2 diabetes. In accordance with the present invention,oligonucleotides of the present invention are tested in the db/db modelof obesity and diabetes.

Seven-week old male C57Bl/6J-Lepr db/db mice (Jackson Laboratory, BarHarbor, Me.) are fed a diet with a fat content of 15-20% and aresubcutaneously injected with one or more of the compositions of theinvention or a control compound at a dose of 25 mg/kg two times per weekfor 4 weeks. Saline-injected animals, leptin receptor wildtypelittermates (i.e. lean littermates) and db/db mice fed a standard rodentdiet serve as controls. After the treatment period, mice are sacrificedand target levels are evaluated in liver, brown adipose tissue (BAT) andwhite adipose tissue (WAT). RNA isolation and target mRNA expressionlevel quantitation are performed as described by other examples herein.

After the treatment period, mice are sacrificed and target levels areevaluated in liver, brown adipose tissue (BAT) and white adipose tissue(WAT). RNA isolation and target mRNA expression level quantitation areperformed as described by other examples herein.

To assess the physiological effects resulting from inhibition of targetmRNA, the db/db mice that receive treatment are further evaluated at theend of the treatment period for serum lipids, serum free fatty acids,serum cholesterol (CHOL), liver triglycerides, fat tissue triglyceridesand liver enzyme levels. Hepatic steatosis, or clearing of lipids fromthe liver, is assessed by measuring the liver triglyceride content.Hepatic steatosis is also assessed by routine histological analysis offrozen liver tissue sections stained with oil red O stain, which iscommonly used to visualize lipid deposits, and counterstained withhematoxylin and eosin, to visualize nuclei and cytoplasm, respectively.

The effects of target inhibition on glucose and insulin metabolism arealso evaluated in the db/db mice treated with the compositions of theinvention. Plasma glucose is measured at the start of the treatment andafter 2 weeks and 4 weeks of treatment. Plasma insulin is similarlymeasured at the beginning of the treatment, and following 2 weeks and 4weeks of treatment. Glucose and insulin tolerance tests are alsoadministered in fed and fasted mice. Mice receive intraperitonealinjections of either glucose or insulin, and the blood glucose levelsare measured before the insulin or glucose challenge and 15, 30, 60, 90and 120 minutes following the injection.

To assess the metabolic rate of db/db mice treated with the compositionsof the invention, the respiratory quotient and oxygen consumption of themice is also measured.

The db/db mice that receive treatment are further evaluated at the endof the treatment period for the effects of target inhibition on theexpression genes that participate in lipid metabolism, cholesterolbiosynthesis, fatty acid oxidation, fatty acid storage, gluconeogenesisand glucose metabolism. These genes include, but are not limited to,HMG-CoA reductase, acetyl-CoA carboxylase 1 and acetyl-CoA carboxylase2, carnitine palmitoyltransferase I and glycogen phosphorylase,glucose-6-phosphatase and phosphoenolpyruvate carboxykinase 1,lipoprotein lipase and hormone sensitive lipase. mRNA levels in liverand white and brown adipose tissue are quantitated by real-time PCR asdescribed in other examples herein, employing primer-probe sets that aregenerated using published sequences of each gene of interest.

EXAMPLE 40

Lean Mice on a Standard Rodent Diet

C57Bl/6 mice are maintained on a standard rodent diet and are used ascontrol (lean) animals. In a further embodiment of the presentinvention, the compositions of the invention are tested in normal, leananimals.

Seven-week old male C57Bl/6 mice are fed a diet with a fat content of 4%and are subcutaneously injected with one or more of the compositions ofthe invention or control compounds at a dose of 25 mg/kg two times perweek for 4 weeks. Saline-injected animals serve as a control. After thetreatment period, mice are sacrificed and target levels are evaluated inliver, brown adipose tissue (BAT) and white adipose tissue (WAT). RNAisolation and target mRNA expression level quantitation are performed asdescribed by other examples herein.

After the treatment period, mice are sacrificed and target levels areevaluated in liver, brown adipose tissue (BAT) and white adipose tissue(WAT). RNA isolation and target mRNA expression level quantitation areperformed as described by other examples herein.

To assess the physiological effects resulting from inhibition of targetmRNA, the lean mice that receive treatment are further evaluated at theend of the treatment period for serum lipids, serum free fatty acids,serum cholesterol (CHOL), liver triglycerides, fat tissue triglyceridesand liver enzyme levels. Hepatic steatosis, or clearing of lipids fromthe liver, is assessed by measuring the liver triglyceride content.Hepatic steatosis is also assessed by routine histological analysis offrozen liver tissue sections stained with oil red O stain, which iscommonly used to visualize lipid deposits, and counterstained withhematoxylin and eosin, to visualize nuclei and cytoplasm, respectively.

The effects of target inhibition on glucose and insulin metabolism arealso evaluated in the lean mice treated with the compositions of theinvention. Plasma glucose is measured at the start of the treatment andafter 2 weeks and 4 weeks of treatment. Plasma insulin is similarlymeasured at the beginning of the treatment, and following 2 weeks and 4weeks of treatment. Glucose and insulin tolerance tests are alsoadministered in fed and fasted mice. Mice receive intraperitonealinjections of either glucose or insulin, and the blood glucose levelsare measured before the insulin or glucose challenge and 15, 30, 60, 90and 120 minutes following the injection.

To assess the metabolic rate of lean mice treated with the compositionsof the invention, the respiratory quotient and oxygen consumption of themice is also measured.

The lean mice that received treatment are further evaluated at the endof the treatment period for the effects of target inhibition on theexpression genes that participate in lipid metabolism, cholesterolbiosynthesis, fatty acid oxidation, fatty acid storage, gluconeogenesisand glucose metabolism. These genes include, but are not limited to,HMG-CoA reductase, acetyl-CoA carboxylase 1 and acetyl-CoA carboxylase2, carnitine palmitoyltransferase I and glycogen phosphorylase,glucose-6-phosphatase and phosphoenolpyruvate carboxykinase 1,lipoprotein lipase and hormone sensitive lipase. mRNA levels in liverand white and brown adipose tissue are quantitated by real-time PCR asdescribed in other examples herein, employing primer-probe sets that aregenerated using published sequences of each gene of interest.

EXAMPLE 41

Chemically Modified siRNA Targeted to PTEN: in Vivo Study

Six- to seven-week old Balb/c mice (Jackson Laboratory, Bar Harbor, Me.)were injected with compounds targeted to PTEN. Each treatment group wascomprised of four animals. Animals were dosed via intraperitonealinjection twice per day for 4.5 days, for a total of 9 doses per animal.Saline-injected animals served as negative controls. Animals weresacrificed 6 hours after the last dose of oligonucleotide wasadministered, and plasma samples and tissues were harvested. Targetreduction in liver was also measured at the conclusion of the study.

Two doses of each treatment were tested. Treatment with ISIS 116847(5′-CTGCTAGCCTCTGGATTTGA-3′, SEQ ID NO: 119), a 5-10-5 gapmer wasadministered at doses of 12.5 mg/kg twice daily or at 6.25 mg/kg twicedaily. The siRNA compounds described below were administered at doses of25 mg/kg twice daily or 6.25 mg/kg twice daily. Each siRNA is composedof an antisense and complement strand as described in previous examples,with the antisense strand targeted to mouse PTEN. ISIS 116847 and all ofthe siRNAs of this experiment also have perfect complementarity withhuman PTEN.

An siRNA duplex targeted to PTEN15 comprised of antisense strand ISIS341391 (5′-UUGUCUCUGGUCCUUACUU-3′, SEQ ID NO: 120) and the sense strandISIS 341401 (5′-AAGUAAGGACCAGAGACAA-3′, SEQ ID NO: 121). Both strands ofthe ISIS 341391/341401 duplex are comprised of ribonucleosides withphosphodiester internucleoside linkages.

Another siRNA duplex targeted to PTEN is comprised of antisense strandISIS 359995 (5′-UUGUCUCUGGUCCUUACUU-3′, SEQ ID NO: 122) and the sensestrand ISIS 359996 (5′-AAGUAAGGACCAGAGACAA-3′, SEQ ID NO: 123). Bothstrands of the ISIS 359995/359996 duplex are comprised of alternating2′-O—CH3 modified and 2′-F modified nucleosides with a phosphodiesterbackbone. 2′-F nucleosides are indicated with bold type.

PTEN mRNA levels in liver were measured at the end of the study usingreal-time PCR and RiboGreen™ RNA quantification reagent (MolecularProbes, Inc. Eugene, Oreg.) as taught in previous examples above. PTENmRNA levels were determined relative to total RNA (using Ribogreen) orGAPDH expression, prior to normalization to saline-treated control.Results are presented in Table 4 as the average % inhibition of mRNAexpression for each treatment group, normalized to saline-injectedcontrol.

TABLE 4 Target reduction by chemically modified siRNAs targeted to PTENin mouse liver Dose (mg/kg, administered % Inhibition Treatment 2x/day)Ribogreen GAPDH ISIS 116847 12.5 92 95 6.25 92 95 ISIS 341391/341401 2512 21 6.25 2 9 ISIS 359995/359996 25 6 13 6.25 5 13

As shown in Table 4, all oligonucleotides targeted to PTEN caused areduction in mRNA levels in liver as compared to saline-treated control.The mRNA levels measured for the ISIS 341391/341401 duplex are alsosuggestive of dose-dependent inhibition.

The effects of treatment with the RNA duplexes on plasma glucose levelswere evaluated in the mice treated as described above. Approximateaverage plasma glucose is presented in Table 5 for each treatment group.

TABLE 5 Effects of chemically modified siRNAs targeted to PTEN on plasmaglucose levels in normal mice Dose (mg/kg, administered Plasma glucoseTreatment 2x/day) (mg/dL) Saline N/A 186 ISIS 116847 12.5 169 6.25 166ISIS 341391/341401 25 159 6.25 182 ISIS 359996/359995 25 182 6.25 169

To assess the physiological effects resulting from in vivo siRNAtargeted to PTEN mRNA, the mice were evaluated at the end of thetreatment period for plasma triglycerides, plasma cholesterol, andplasma transaminase levels. Plasma cholesterol levels from animalstreated with either dose of ISIS 116847 were increased about 20% overlevels measured for saline-treated animals. Conversely, the cholesterollevels measured for animals treated with either the 25 mg/kg or the 6.25mg/kg doses of the ISIS 341391/341401 duplex were decreased about 12% ascompared to saline-treated controls. The ISIS 359996/359995 duplex didnot cause significant alterations in cholesterol levels. All of thetreatment groups showed decreased plasma triglycerides as compared tosaline-treated control, regardless of treatment dose.

Increases in the transaminases ALT and AST can indicate hepatotoxicity.The transaminase levels measured for mice treated with the siRNAduplexes were not elevated to a level indicative of hepatotoxicity withrespect to saline treated control. Treatment with 12.5 mg/kg doses ofISIS 116847 caused approximately 7-fold and 3-fold increases in ALT andAST levels, respectively. Treatment with the lower doses (6.25 mg/kg) ofISIS 116847 caused approximately 4-fold and 2-fold increases in ALT andAST levels, respectively.

At the end of the study, liver, white adipose tissue (WAT), spleen, andkidney were harvested from animals treated with the oligomeric compoundsand were weighed to assess gross organ alterations. Approximate averagetissue weights for each treatment group are presented in Table 6.

TABLE 6 Effects of chemically modified siRNAs targeted to PTEN on tissueweight in normal mice Dose (mg/kg, administered Liver WAT Spleen KidneyTreatment 2x/day) Tissue weight (g) Saline N/A 1.0 0.5 0.1 0.3 ISIS116847 12.5 1.1 0.4 0.1 0.3 6.25 1.1 0.4 0.1 0.3 ISIS 25 1.0 0.3 0.1 0.3341391/341401 6.25 0.9 0.4 0.1 0.3 ISIS 25 1.1 0.4 0.1 0.3 359996/3599956.25 1.0 0.3 0.1 0.4

As shown in Table 6, treatment with antisense oligonucleotides or siRNAduplexes targeted to PTEN did not substantially alter liver, WAT,spleen, or kidney weights in normal mice as compared to the organweights of mice treated with saline alone.

EXAMPLE 42

Stability of Alternating 2′-O-methyl/2′-fluoro siRNA Constructs in MousePlasma

Intact duplex RNA was analyzed from diluted mouse-plasma using anextraction and capillary electrophoresis method similar to thosepreviously described (Leeds, J. M., et al., 1996, Anal. Biochem., 235,36-43; Geary, R. S., et al., 1999, Anal. Biochem., 274, 241-248..Heparin-treated mouse plasma, from 3-6 month old female Balb/c mice(Charles River Labs) was thawed from −80° C. and diluted to 25% (v/v)with phosphate buffered saline (140 mM NaCl, 3 mM KCl, 2 mM potassiumphosphate, 10 mM sodium phosphate). Approximately 10 nmol ofpre-annealed siRNA, at a concentration of 100 μM, was added to the 25%plasma and incubated at 37° C. for 0, 15, 30, 45, 60, 120, 180, 240,360, and 420 minutes. Aliquots were removed at the indicated time,treated with EDTA to a final concentration of 2 mM, and placed on ice at0° C. until analyzed by capillary gel electrophoresis (Beckman P/ACEMDQ-UV with eCap DNA Capillary tube). The area of the siRNA duplex peakwas measured and used to calculate the percent of intact siRNAremaining. Adenosine triphosphate (ATP) was added at a concentration of2.5 mM to each injection as an internal calibration standard. A zerotime point was taken by diluting siRNA in phosphate buffered salinefollowed by capillary electrophoresis. Percent intact siRNA was plottedagainst time, allowing the calculation of a pseudo first-orderhalf-life. Results are shown in Table 7.

TABLE 7 Stability of alternating 2′-O-methyl/2′-fluoro siRNA constructsin mouse plasma Time (minutes) Construct 0 15 30 45 60 120 180 240 360338918_338943 76.98 71.33 49.77 40.85 27.86 22.53 14.86 4.18 0351831_351832 82.42 81.05 79.56 77.64 75.54 75.55 75.56 75.55 75

The parent (unmodified) construct is approximately 50% degraded after 30minutes and nearly gone after 4 hours (completely gone at 6 hours). Incontrast, the alternating 2′-O-methyl/2′-fluoro construct remainsrelatively unchanged and 75% remains even after 6 hours.

What is claimed:
 1. A method of reducing target messenger RNA in a cellcomprising contacting the cell with a composition comprising first andsecond chemically synthesized oligomeric compounds, wherein: the firstoligomeric compound is fully complementary to and capable of hybridizingto the second oligomeric compound and to the target messenger RNA; eachof the first and second oligomeric compounds independently comprisesfrom 17 to 23 nucleosides; and the first oligomeric compound comprisesat least one motif selected from F(SF)_(n)S_(nn) where n is from 2 toabout 20, nn is 0 or 1, one of F and S is a 2′-F modified nucleoside andthe other of F and S is a 2′-O—CH₃ modified nucleoside; thereby reducingthe target messenger RNA in the cell.
 2. The method of claim 1 whereineach F is a 2′-O—CH₃ modified nucleoside.
 3. The method of claim 1wherein each F is a 2′-F modified nucleoside.
 4. The method of claim 1wherein said first oligomeric compound further comprises a 5′-phosphategroup.
 5. The method of claim 1 wherein said second oligomeric compoundfurther comprises a 5′-phosphate group.
 6. The method of claim 1 whereineach of said first and said second oligomeric compounds independently,comprise a 5′-phosphate group.
 7. The method of claim 1 wherein saidfirst oligomeric compound comprises a 3′-terminal OH group.
 8. Themethod of claim 1 wherein said first and said second oligomericcompounds comprise only phosphodiester internucleoside linking groups.9. The method of claim 1 wherein said first and said second oligomericcompounds comprise only phosphorothioate internucleoside linking groups.10. The method of claim 1 wherein said first oligomeric compoundcomprises only phosphodiester internucleoside linking groups and saidsecond oligomeric compound comprises only phosphorothioateinternucleoside linking groups; or said first oligomeric compoundcomprises only phosphorothioate internucleoside linking groups and saidsecond oligomeric compound comprises only phosphodiester internucleosidelinking groups.
 11. The method of claim 1 wherein said first oligomericcompound comprises only phosphorothioate internucleoside linking groupsand said second oligomeric compound comprises only phosphodiesterinternucleoside linking groups.
 12. The method of claim 1 wherein saidfirst and said second oligomeric compounds comprise internucleosidelinking groups that are each independently selected from phosphodiesterand phosphorothioate internucleoside linking groups.
 13. The method ofclaim 1 wherein said first and said second oligomeric compounds compriseinternucleoside linking groups that are each independently selected fromphosphodiester, phosphorothioate, chiral phosphorothioate,phosphorodithioate, phosphotriester, aminoalkylphosphotriester, methylphosphonate, alkyl phosphonate, 5′-alkylene phosphonate, chiralphosphonate, phosphinate, phosphoramidate, 3′-amino phosphoramidate,aminoalkylphosphoramidate, thionophosphoramidate,thionoalkylphosphonate, thionoalkylphosphotriester, selenophosphate andboranophosphate.
 14. The method of claim 1 further comprising oneconjugate group.
 15. The method of claim 1 wherein at least one of saidfirst and said second oligomeric compounds further comprises at leastone conjugate group attached at the 3′-end or the 5′-end.
 16. The methodof claim 1 wherein at least one of said first and said second oligomericcompounds further comprises at least one terminal cap moiety attached atthe 3′-end or the 5′-end or one terminal cap moiety attached at the3′-end and a second terminal cap moiety attached at the 5′-end.
 17. Themethod of claim 16 wherein each of said terminal cap moieties is aninverted deoxy abasic moiety.
 18. The method of claim 16 wherein saidsecond oligomeric compound is a sense strand comprising a terminal capmoiety at 3′-end, the 5′-end or one terminal cap at the 3′-end and asecond terminal cap at the 5′-end.
 19. The method of claim 18 whereinsaid terminal cap moiety is an inverted deoxy abasic moiety.
 20. Themethod of claim 1 wherein said first and said second oligomericcompounds are a complementary pair of siRNA oligonucleotides.
 21. Themethod of claim 1 wherein said first oligomeric compound is an antisenseoligonucleotide.